reftable: explicitly store update_index per ref

Add an update_index to every reference in a reftable, storing the
exact transaction that last modified the reference.  This is necessary
to fix some merge race conditions.

Consider updates at T1, T3 are present in two reftables.  Compacting
these will create a table with range [T1,T3].  If T2 arrives during
or after the compaction its impossible for readers to know how to
merge the [T1,T3] table with the T2 table.

With an explicit update_index per reference, MergedReftable is able to
individually sort each reference, merging individual entries at T3
from [T1,T3] ahead of identically named entries appearing in T2.

Change-Id: Ie4065d4176a5a0207dcab9696ae05d086e042140

Documentation/technical/reftable.md

     varint( prefix_length )
     varint( (suffix_length << 3) | value_type )
     suffix
+    varint( update_index_delta )
     value?
 
 The `prefix_length` field specifies how many leading bytes of the
 The `suffix_length` value provides the number of bytes available in
 `suffix` to copy from `suffix` to complete the reference name.
 
+The `update_index` that last modified the reference can be obtained by
+adding `update_index_delta` to the `min_update_index` from the file
+header: `min_update_index + update_index_delta`.
+
 The `value` follows.  Its format is determined by `value_type`, one of
 the following:
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/MergedReftableTest.java

 		}
 	}
 
+	@Test
+	public void missedUpdate() throws IOException {
+		ByteArrayOutputStream buf = new ByteArrayOutputStream();
+		ReftableWriter writer = new ReftableWriter()
+				.setMinUpdateIndex(1)
+				.setMaxUpdateIndex(3)
+				.begin(buf);
+		writer.writeRef(ref("refs/heads/a", 1), 1);
+		writer.writeRef(ref("refs/heads/c", 3), 3);
+		writer.finish();
+		byte[] base = buf.toByteArray();
+
+		byte[] delta = write(Arrays.asList(
+				ref("refs/heads/b", 2),
+				ref("refs/heads/c", 4)),
+				2);
+		MergedReftable mr = merge(base, delta);
+		try (RefCursor rc = mr.allRefs()) {
+			assertTrue(rc.next());
+			assertEquals("refs/heads/a", rc.getRef().getName());
+			assertEquals(id(1), rc.getRef().getObjectId());
+			assertEquals(1, rc.getUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals("refs/heads/b", rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(2, rc.getUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals("refs/heads/c", rc.getRef().getName());
+			assertEquals(id(3), rc.getRef().getObjectId());
+			assertEquals(3, rc.getUpdateIndex());
+		}
+	}
+
 	@Test
 	public void compaction() throws IOException {
 		List<Ref> delta1 = Arrays.asList(
 	}
 
 	private byte[] write(Collection<Ref> refs) throws IOException {
+		return write(refs, 1);
+	}
+
+	private byte[] write(Collection<Ref> refs, long updateIndex)
+			throws IOException {
 		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
-		ReftableWriter writer = new ReftableWriter().begin(buffer);
-		for (Ref r : RefComparator.sort(refs)) {
-			writer.writeRef(r);
-		}
-		writer.finish();
+		new ReftableWriter()
+				.setMinUpdateIndex(updateIndex)
+				.setMaxUpdateIndex(updateIndex)
+				.begin(buffer)
+				.sortAndWriteRefs(refs)
+				.finish();
 		return buffer.toByteArray();
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java

 	@Test
 	public void estimateCurrentBytesOneRef() throws IOException {
 		Ref exp = ref(MASTER, 1);
-		int expBytes = 24 + 4 + 5 + 3 + MASTER.length() + 20 + 68;
+		int expBytes = 24 + 4 + 5 + 4 + MASTER.length() + 20 + 68;
 
 		byte[] table;
 		ReftableConfig cfg = new ReftableConfig();
 		cfg.setIndexObjects(false);
 		cfg.setMaxIndexLevels(1);
 
-		int expBytes = 139654;
+		int expBytes = 147860;
 		byte[] table;
 		ReftableWriter writer = new ReftableWriter().setConfig(cfg);
 		try (ByteArrayOutputStream buf = new ByteArrayOutputStream()) {
 	public void oneIdRef() throws IOException {
 		Ref exp = ref(MASTER, 1);
 		byte[] table = write(exp);
-		assertEquals(24 + 4 + 5 + 3 + MASTER.length() + 20 + 68, table.length);
+		assertEquals(24 + 4 + 5 + 4 + MASTER.length() + 20 + 68, table.length);
 
 		ReftableReader t = read(table);
 		try (RefCursor rc = t.allRefs()) {
 	public void oneTagRef() throws IOException {
 		Ref exp = tag(V1_0, 1, 2);
 		byte[] table = write(exp);
-		assertEquals(24 + 4 + 5 + 2 + V1_0.length() + 40 + 68, table.length);
+		assertEquals(24 + 4 + 5 + 3 + V1_0.length() + 40 + 68, table.length);
 
 		ReftableReader t = read(table);
 		try (RefCursor rc = t.allRefs()) {
 		Ref exp = sym(HEAD, MASTER);
 		byte[] table = write(exp);
 		assertEquals(
-				24 + 4 + 5 + 2 + HEAD.length() + 1 + MASTER.length() + 68,
+				24 + 4 + 5 + 2 + HEAD.length() + 2 + MASTER.length() + 68,
 				table.length);
 
 		ReftableReader t = read(table);
 		String name = "refs/heads/gone";
 		Ref exp = newRef(name);
 		byte[] table = write(exp);
-		assertEquals(24 + 4 + 5 + 2 + name.length() + 68, table.length);
+		assertEquals(24 + 4 + 5 + 3 + name.length() + 68, table.length);
 
 		ReftableReader t = read(table);
 		try (RefCursor rc = t.allRefs()) {
 
 		writer.finish();
 		byte[] table = buffer.toByteArray();
-		assertEquals(245, table.length);
+		assertEquals(247, table.length);
 
 		ReftableReader t = read(table);
 		try (RefCursor rc = t.allRefs()) {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
 			assertEquals(id(1), rc.getRef().getObjectId());
+			assertEquals(1, rc.getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals(NEXT, rc.getRef().getName());
 			writer.finish();
 			fail("expected BlockSizeTooSmallException");
 		} catch (BlockSizeTooSmallException e) {
-			assertEquals(84, e.getMinimumBlockSize());
+			assertEquals(85, e.getMinimumBlockSize());
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockReader.java

 		return readVarint64();
 	}
 
+	long readUpdateIndexDelta() {
+		return readVarint64();
+	}
+
 	Ref readRef() throws IOException {
 		String name = RawParseUtils.decode(UTF_8, nameBuf, 0, nameLen);
 		switch (valueType & VALUE_TYPE_MASK) {
 	void skipValue() {
 		switch (blockType) {
 		case REF_BLOCK_TYPE:
+			readVarint64(); // update_index_delta
 			switch (valueType & VALUE_TYPE_MASK) {
 			case VALUE_NONE:
 				return;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockWriter.java

 
 	static class RefEntry extends Entry {
 		final Ref ref;
+		final long updateIndexDelta;
 
-		RefEntry(Ref ref) {
+		RefEntry(Ref ref, long updateIndexDelta) {
 			super(nameUtf8(ref));
 			this.ref = ref;
+			this.updateIndexDelta = updateIndexDelta;
 		}
 
 		@Override
 
 		@Override
 		int valueSize() {
+			int n = computeVarintSize(updateIndexDelta);
 			switch (valueType()) {
 			case VALUE_NONE:
-				return 0;
+				return n;
 			case VALUE_1ID:
-				return OBJECT_ID_LENGTH;
+				return n + OBJECT_ID_LENGTH;
 			case VALUE_2ID:
-				return 2 * OBJECT_ID_LENGTH;
+				return n + 2 * OBJECT_ID_LENGTH;
 			case VALUE_SYMREF:
 				if (ref.isSymbolic()) {
 					int nameLen = nameUtf8(ref.getTarget()).length;
-					return computeVarintSize(nameLen) + nameLen;
+					return n + computeVarintSize(nameLen) + nameLen;
 				}
 			}
 			throw new IllegalStateException();
 
 		@Override
 		void writeValue(ReftableOutputStream os) throws IOException {
+			os.writeVarint(updateIndexDelta);
 			switch (valueType()) {
 			case VALUE_NONE:
 				return;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/MergedReftable.java

 
 	@Override
 	public RefCursor seekRef(String name) throws IOException {
-		if (name.endsWith("/")) { //$NON-NLS-1$
-			return seekRefPrefix(name);
-		}
-		return seekSingleRef(name);
-	}
-
-	private RefCursor seekRefPrefix(String name) throws IOException {
 		MergedRefCursor m = new MergedRefCursor();
 		for (int i = 0; i < tables.length; i++) {
 			m.add(new RefQueueEntry(tables[i].seekRef(name), i));
 		return m;
 	}
 
-	private RefCursor seekSingleRef(String name) throws IOException {
-		// Walk the tables from highest priority (end of list) to lowest.
-		// As soon as the reference is found (queue not empty), all lower
-		// priority tables are irrelevant as current table shadows them.
-		MergedRefCursor m = new MergedRefCursor();
-		for (int i = tables.length - 1; i >= 0 && m.queue.isEmpty(); i--) {
-			m.add(new RefQueueEntry(tables[i].seekRef(name), i));
-		}
-		return m;
-	}
-
 	@Override
 	public RefCursor byObjectId(AnyObjectId name) throws IOException {
 		MergedRefCursor m = new MergedRefCursor();
 		private final PriorityQueue<RefQueueEntry> queue;
 		private RefQueueEntry head;
 		private Ref ref;
+		private long updateIndex;
 
 		MergedRefCursor() {
 			queue = new PriorityQueue<>(queueSize(), RefQueueEntry::compare);
 				}
 
 				ref = t.rc.getRef();
+				updateIndex = t.rc.getUpdateIndex();
 				boolean include = includeDeletes || !t.rc.wasDeleted();
 				skipShadowedRefs(ref.getName());
 				add(t);
 			return ref;
 		}
 
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
 		@Override
 		public void close() {
+			if (head != null) {
+				head.rc.close();
+				head = null;
+			}
 			while (!queue.isEmpty()) {
 				queue.remove().rc.close();
 			}
 	private static class RefQueueEntry {
 		static int compare(RefQueueEntry a, RefQueueEntry b) {
 			int cmp = a.name().compareTo(b.name());
+			if (cmp == 0) {
+				// higher updateIndex shadows lower updateIndex.
+				cmp = Long.signum(b.updateIndex() - a.updateIndex());
+			}
 			if (cmp == 0) {
 				// higher index shadows lower index, so higher index first.
 				cmp = b.stackIdx - a.stackIdx;
 		String name() {
 			return rc.getRef().getName();
 		}
+
+		long updateIndex() {
+			return rc.getUpdateIndex();
+		}
 	}
 
 	private class MergedLogCursor extends LogCursor {

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java

 	/** @return reference at the current position. */
 	public abstract Ref getRef();
 
+	/** @return updateIndex that last modified the current reference, */
+	public abstract long getUpdateIndex();
+
 	/** @return {@code true} if the current reference was deleted. */
 	public boolean wasDeleted() {
 		Ref r = getRef();

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableCompactor.java

 	private void mergeRefs(MergedReftable mr) throws IOException {
 		try (RefCursor rc = mr.allRefs()) {
 			while (rc.next()) {
-				writer.writeRef(rc.getRef());
+				writer.writeRef(rc.getRef(), rc.getUpdateIndex());
 			}
 		}
 	}

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableReader.java

 		private final boolean prefix;
 
 		private Ref ref;
+		private long updateIndex;
 		BlockReader block;
 
 		RefCursorImpl(long scanEnd, byte[] match, boolean prefix) {
 					return false;
 				}
 
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
 				ref = block.readRef();
 				if (!includeDeletes && wasDeleted()) {
 					continue;
 			return ref;
 		}
 
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
 		@Override
 		public void close() {
 			// Do nothing.
 		private final ObjectId match;
 
 		private Ref ref;
+		private long updateIndex;
 		private int listIdx;
 
 		private LongList blockPos;
 				}
 
 				block.parseKey();
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
 				ref = block.readRef();
 				ObjectId id = ref.getObjectId();
 				if (id != null && match.equals(id)
 			return ref;
 		}
 
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
 		@Override
 		public void close() {
 			// Do nothing.

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableWriter.java

 	public ReftableWriter sortAndWriteRefs(Collection<Ref> refsToPack)
 			throws IOException {
 		Iterator<RefEntry> itr = refsToPack.stream()
-				.map(RefEntry::new)
+				.map(r -> new RefEntry(r, maxUpdateIndex - minUpdateIndex))
 				.sorted(Entry::compare)
 				.iterator();
 		while (itr.hasNext()) {
 	 *             if reftable cannot be written.
 	 */
 	public void writeRef(Ref ref) throws IOException {
-		long blockPos = refs.write(new RefEntry(ref));
+		writeRef(ref, maxUpdateIndex);
+	}
+
+	/**
+	 * Write one reference to the reftable.
+	 * <p>
+	 * References must be passed in sorted order.
+	 *
+	 * @param ref
+	 *            the reference to store.
+	 * @param updateIndex
+	 *            the updateIndex that modified this reference. Must be
+	 *            {@code >= minUpdateIndex} for this file.
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public void writeRef(Ref ref, long updateIndex) throws IOException {
+		if (updateIndex < minUpdateIndex) {
+			throw new IllegalArgumentException();
+		}
+		long d = updateIndex - minUpdateIndex;
+		long blockPos = refs.write(new RefEntry(ref, d));
 		indexRef(ref, blockPos);
 	}