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

@@ -243,6 +243,7 @@ its value(s). Records are formatted as:
     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
@@ -258,6 +259,10 @@ Recovering a reference name from any `ref_record` is a simple concat:
 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

@@ -261,6 +261,41 @@ public void oneTableSeek() throws IOException {
 		}
 	}
 
+	@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(
@@ -322,12 +357,18 @@ private byte[] write(Ref... refs) throws IOException {
 	}
 
 	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);
+		new ReftableWriter()
-		for (Ref r : RefComparator.sort(refs)) {
+				.setMinUpdateIndex(updateIndex)
-			writer.writeRef(r);
+				.setMaxUpdateIndex(updateIndex)
-		}
+				.begin(buffer)
-		writer.finish();
+				.sortAndWriteRefs(refs)
+				.finish();
 		return buffer.toByteArray();
 	}
 

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

@@ -126,7 +126,7 @@ public void emptyVirtualTableFromRefs() throws IOException {
 	@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();
@@ -155,7 +155,7 @@ public void estimateCurrentBytesWithIndex() throws IOException {
 		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()) {
@@ -174,7 +174,7 @@ public void estimateCurrentBytesWithIndex() throws IOException {
 	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()) {
@@ -203,7 +203,7 @@ public void oneIdRef() throws IOException {
 	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()) {
@@ -224,7 +224,7 @@ public void oneSymbolicRef() throws IOException {
 		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);
@@ -281,7 +281,7 @@ public void oneDeletedRef() throws IOException {
 		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()) {
@@ -425,13 +425,14 @@ public void withReflog() throws IOException {
 
 		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());
@@ -636,7 +637,7 @@ public void nameTooLongDoesNotWrite() throws IOException {
 			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

@@ -166,6 +166,10 @@ long readPositionFromIndex() throws IOException {
 		return readVarint64();
 	}
 
+	long readUpdateIndexDelta() {
+		return readVarint64();
+	}
+
 	Ref readRef() throws IOException {
 		String name = RawParseUtils.decode(UTF_8, nameBuf, 0, nameLen);
 		switch (valueType & VALUE_TYPE_MASK) {
@@ -490,6 +494,7 @@ private int scanToKey(byte[] key, int rPtr, int rIdx, int rCmp) {
 	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

@@ -354,10 +354,12 @@ void writeValue(ReftableOutputStream os) {
 
 	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
@@ -380,17 +382,18 @@ int valueType() {
 
 		@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();
@@ -398,6 +401,7 @@ int valueSize() {
 
 		@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

@@ -100,13 +100,6 @@ public RefCursor allRefs() throws IOException {
 
 	@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));
@@ -114,17 +107,6 @@ private RefCursor seekRefPrefix(String name) throws IOException {
 		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();
@@ -168,6 +150,7 @@ private class MergedRefCursor extends RefCursor {
 		private final PriorityQueue<RefQueueEntry> queue;
 		private RefQueueEntry head;
 		private Ref ref;
+		private long updateIndex;
 
 		MergedRefCursor() {
 			queue = new PriorityQueue<>(queueSize(), RefQueueEntry::compare);
@@ -205,6 +188,7 @@ public boolean next() throws IOException {
 				}
 
 				ref = t.rc.getRef();
+				updateIndex = t.rc.getUpdateIndex();
 				boolean include = includeDeletes || !t.rc.wasDeleted();
 				skipShadowedRefs(ref.getName());
 				add(t);
@@ -239,8 +223,17 @@ public Ref getRef() {
 			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();
 			}
@@ -250,6 +243,10 @@ public void 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;
@@ -268,6 +265,10 @@ static int compare(RefQueueEntry a, RefQueueEntry b) {
 		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

@@ -61,6 +61,9 @@ public abstract class RefCursor implements AutoCloseable {
 	/** @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

@@ -220,7 +220,7 @@ public Stats getStats() {
 	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

@@ -455,6 +455,7 @@ private class RefCursorImpl extends RefCursor {
 		private final boolean prefix;
 
 		private Ref ref;
+		private long updateIndex;
 		BlockReader block;
 
 		RefCursorImpl(long scanEnd, byte[] match, boolean prefix) {
@@ -483,6 +484,7 @@ public boolean next() throws IOException {
 					return false;
 				}
 
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
 				ref = block.readRef();
 				if (!includeDeletes && wasDeleted()) {
 					continue;
@@ -496,6 +498,11 @@ public Ref getRef() {
 			return ref;
 		}
 
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
 		@Override
 		public void close() {
 			// Do nothing.
@@ -574,6 +581,7 @@ private class ObjCursorImpl extends RefCursor {
 		private final ObjectId match;
 
 		private Ref ref;
+		private long updateIndex;
 		private int listIdx;
 
 		private LongList blockPos;
@@ -647,6 +655,7 @@ public boolean next() throws IOException {
 				}
 
 				block.parseKey();
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
 				ref = block.readRef();
 				ObjectId id = ref.getObjectId();
 				if (id != null && match.equals(id)
@@ -661,6 +670,11 @@ public Ref getRef() {
 			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

@@ -214,7 +214,7 @@ public ReftableWriter begin(OutputStream os) throws IOException {
 	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()) {
@@ -236,7 +236,28 @@ public ReftableWriter sortAndWriteRefs(Collection<Ref> refsToPack)
 	 *             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);
 	}