go/store/nbs: store.go: Clean up how we update hasCache so that we only update it after successfully writing the memtable.

go/libraries/doltcore/doltdb/gc_test.go

@@ -16,6 +16,8 @@ package doltdb_test
 
 import (
 	"context"
+	"errors"
+	"os"
 	"testing"
 
 	"github.com/dolthub/go-mysql-server/sql"
@@ -28,7 +30,13 @@ import (
 	"github.com/dolthub/dolt/go/libraries/doltcore/env"
 	"github.com/dolthub/dolt/go/libraries/doltcore/ref"
 	"github.com/dolthub/dolt/go/libraries/doltcore/sqle"
+	"github.com/dolthub/dolt/go/libraries/utils/filesys"
 	"github.com/dolthub/dolt/go/store/hash"
+	"github.com/dolthub/dolt/go/store/nbs"
+	"github.com/dolthub/dolt/go/store/prolly"
+	"github.com/dolthub/dolt/go/store/prolly/tree"
+	"github.com/dolthub/dolt/go/store/types"
+	"github.com/dolthub/dolt/go/store/val"
 )
 
 func TestGarbageCollection(t *testing.T) {
@@ -40,6 +48,8 @@ func TestGarbageCollection(t *testing.T) {
 			testGarbageCollection(t, gct)
 		})
 	}
+
+	t.Run("HasCacheDataCorruption", testGarbageCollectionHasCacheDataCorruptionBugFix)
 }
 
 type stage struct {
@@ -140,3 +150,118 @@ func testGarbageCollection(t *testing.T, test gcTest) {
 	require.NoError(t, err)
 	assert.Equal(t, test.expected, actual)
 }
+
+// In September 2023, we found a failure to handle the `hasCache` in
+// `*NomsBlockStore` appropriately while cleaning up a memtable into which
+// dangling references had been written could result in writing chunks to a
+// database which referenced non-existant chunks.
+//
+// The general pattern was to get new chunk addresses into the hasCache, but
+// not written to the store, and then to have an incoming chunk add a refenece
+// to missing chunk. At that time, we would clear the memtable, since it had
+// invalid chunks in it, but we wouldn't purge the hasCache. Later writes which
+// attempted to reference the chunks which had made it into the hasCache would
+// succeed.
+//
+// One such concrete pattern for doing this is implemented below. We do:
+//
+// 1) Put a new chunk to the database -- C1.
+//
+// 2) Run a GC.
+//
+// 3) Put a new chunk to the database -- C2.
+//
+// 4) Call NBS.Commit() with a stale last hash.Hash. This causes us to cache C2
+// as present in the store, but it does not get written to disk, because the
+// optimistic concurrency control on the value of the current root hash fails.
+//
+// 5) Put a chunk referencing C1 to the database -- R1.
+//
+// 5) Call NBS.Commit(). This causes ErrDanglingRef. C1 was written before the
+// GC and is no longer in the store. C2 is also cleared from the pending write
+// set.
+//
+// 6) Put a chunk referencing C2 to the database -- R2.
+//
+// 7) Call NBS.Commit(). This should fail, since R2 references C2 and C2 is not
+// in the store. However, C2 is in the cache as a result of step #4, and so
+// this does not fail. R2 gets written to disk with a dangling reference to C2.
+func testGarbageCollectionHasCacheDataCorruptionBugFix(t *testing.T) {
+	ctx := context.Background()
+
+	d, err := os.MkdirTemp(t.TempDir(), "hascachetest-")
+	require.NoError(t, err)
+
+	ddb, err := doltdb.LoadDoltDB(ctx, types.Format_DOLT, "file://"+d, filesys.LocalFS)
+	require.NoError(t, err)
+	defer ddb.Close()
+
+	err = ddb.WriteEmptyRepo(ctx, "main", "Aaron Son", "aaron@dolthub.com")
+	require.NoError(t, err)
+
+	root, err := ddb.NomsRoot(ctx)
+	require.NoError(t, err)
+
+	ns := ddb.NodeStore()
+
+	c1 := newIntMap(t, ctx, ns, 1, 1)
+	_, err = ns.Write(ctx, c1.Node())
+	require.NoError(t, err)
+
+	err = ddb.GC(ctx, nil)
+	require.NoError(t, err)
+
+	c2 := newIntMap(t, ctx, ns, 2, 2)
+	_, err = ns.Write(ctx, c2.Node())
+	require.NoError(t, err)
+
+	success, err := ddb.CommitRoot(ctx, c2.HashOf(), c2.HashOf())
+	require.NoError(t, err)
+	require.False(t, success, "committing the root with a last hash which does not match the current root must fail")
+
+	r1 := newAddrMap(t, ctx, ns, "r1", c1.HashOf())
+	_, err = ns.Write(ctx, r1.Node())
+	require.NoError(t, err)
+
+	success, err = ddb.CommitRoot(ctx, root, root)
+	require.True(t, errors.Is(err, nbs.ErrDanglingRef), "committing a reference to just-collected c1 must fail with ErrDanglingRef")
+
+	r2 := newAddrMap(t, ctx, ns, "r2", c2.HashOf())
+	_, err = ns.Write(ctx, r2.Node())
+	require.NoError(t, err)
+
+	success, err = ddb.CommitRoot(ctx, root, root)
+	require.True(t, errors.Is(err, nbs.ErrDanglingRef), "committing a reference to c2, which was erased with the ErrDanglingRef above, must also fail with ErrDanglingRef")
+}
+
+func newIntMap(t *testing.T, ctx context.Context, ns tree.NodeStore, k, v int8) prolly.Map {
+	desc := val.NewTupleDescriptor(val.Type{
+		Enc:      val.Int8Enc,
+		Nullable: false,
+	})
+
+	tb := val.NewTupleBuilder(desc)
+	tb.PutInt8(0, k)
+	keyTuple := tb.Build(ns.Pool())
+
+	tb.PutInt8(0, v)
+	valueTuple := tb.Build(ns.Pool())
+
+	m, err := prolly.NewMapFromTuples(ctx, ns, desc, desc, keyTuple, valueTuple)
+	require.NoError(t, err)
+	return m
+}
+
+func newAddrMap(t *testing.T, ctx context.Context, ns tree.NodeStore, key string, h hash.Hash) prolly.AddressMap {
+	m, err := prolly.NewEmptyAddressMap(ns)
+	require.NoError(t, err)
+
+	editor := m.Editor()
+	err = editor.Add(ctx, key, h)
+	require.NoError(t, err)
+
+	m, err = editor.Flush(ctx)
+	require.NoError(t, err)
+
+	return m
+}

go/store/nbs/generational_chunk_store.go

@@ -16,7 +16,6 @@ package nbs
 
 import (
 	"context"
-	"fmt"
 	"io"
 	"path/filepath"
 	"strings"
@@ -154,18 +153,6 @@ func (gcs *GenerationalNBS) hasMany(recs []hasRecord) (absent hash.HashSet, err
 	return gcs.oldGen.hasMany(recs)
 }
 
-func (gcs *GenerationalNBS) errorIfDangling(ctx context.Context, addrs hash.HashSet) error {
-	absent, err := gcs.HasMany(ctx, addrs)
-	if err != nil {
-		return err
-	}
-	if len(absent) != 0 {
-		s := absent.String()
-		return fmt.Errorf("Found dangling references to %s", s)
-	}
-	return nil
-}
-
 // Put caches c in the ChunkSource. Upon return, c must be visible to
 // subsequent Get and Has calls, but must not be persistent until a call
 // to Flush(). Put may be called concurrently with other calls to Put(),

go/store/nbs/store.go

@@ -705,6 +705,36 @@ func (nbs *NomsBlockStore) putChunk(ctx context.Context, c chunks.Chunk, getAddr
 	return nil
 }
 
+// When we have chunks with dangling references in our memtable, we have to
+// throw away the entire memtable.
+func (nbs *NomsBlockStore) handlePossibleDanglingRefError(err error) {
+	if errors.Is(err, ErrDanglingRef) {
+		nbs.mt = nil
+	}
+}
+
+// Writes to a Dolt database typically involve mutating some tuple maps and
+// then mutating the top-level address map which points to all the branch heads
+// and working sets. Each internal node of the address map can have many
+// references and many of them typically change quite slowly. We keep a cache
+// of recently written references which we know are in the database so that we
+// don't have to check the table file indexes for these  chunks when we write
+// references to them again in the near future.
+//
+// This cache needs to be treated in a principled manner. The integrity checks
+// that we run against the a set of chunks we are attempting to write consider
+// the to-be-written chunks themselves as also being in the database. This is
+// correct, assuming that all the chunks are written at the same time. However,
+// we should not add the results of those presence checks to the cache until
+// those chunks actually land in the database.
+func (nbs *NomsBlockStore) addPendingRefsToHasCache() {
+	for _, e := range nbs.mt.pendingRefs {
+		if e.has {
+			nbs.hasCache.Add(*e.a, struct{}{})
+		}
+	}
+}
+
 func (nbs *NomsBlockStore) addChunk(ctx context.Context, ch chunks.Chunk, addrs hash.HashSet, checker refCheck) (bool, error) {
 	if err := ctx.Err(); err != nil {
 		return false, err
@@ -725,11 +755,10 @@ func (nbs *NomsBlockStore) addChunk(ctx context.Context, ch chunks.Chunk, addrs
 		if addChunkRes == chunkNotAdded {
 			ts, err := nbs.tables.append(ctx, nbs.mt, checker, nbs.hasCache, nbs.stats)
 			if err != nil {
-				if errors.Is(err, ErrDanglingRef) {
-					nbs.mt = nil
-				}
+				nbs.handlePossibleDanglingRefError(err)
 				return false, err
 			}
+			nbs.addPendingRefsToHasCache()
 			nbs.tables = ts
 			nbs.mt = newMemTable(nbs.mtSize)
 			addChunkRes = nbs.mt.addChunk(a, ch.Data())
@@ -757,7 +786,6 @@ type refCheck func(reqs []hasRecord) (hash.HashSet, error)
 func (nbs *NomsBlockStore) errorIfDangling(root hash.Hash, checker refCheck) error {
 	if !root.IsEmpty() {
 		a := addr(root)
-		// We use |Get| here, since it updates recency of the entry.
 		if _, ok := nbs.hasCache.Get(a); !ok {
 			var hr [1]hasRecord
 			hr[0].a = &a
@@ -771,32 +799,6 @@ func (nbs *NomsBlockStore) errorIfDangling(root hash.Hash, checker refCheck) err
 			nbs.hasCache.Add(a, struct{}{})
 		}
 	}
-
-	if nbs.mt == nil || nbs.mt.pendingRefs == nil {
-		return nil // no pending refs to check
-	}
-
-	for i := range nbs.mt.pendingRefs {
-		// All of these are going to be |Add|ed after the call.  We use
-		// |Contains| to check here so the frequency count only gets
-		// bumped once.
-		if nbs.hasCache.Contains(*nbs.mt.pendingRefs[i].a) {
-			nbs.mt.pendingRefs[i].has = true
-		}
-	}
-
-	sort.Sort(hasRecordByPrefix(nbs.mt.pendingRefs))
-	absent, err := checker(nbs.mt.pendingRefs)
-	if err != nil {
-		return err
-	} else if absent.Size() > 0 {
-		return fmt.Errorf("%w: found dangling references to %s", ErrDanglingRef, absent.String())
-	}
-
-	for _, e := range nbs.mt.pendingRefs {
-		nbs.hasCache.Add(*e.a, struct{}{})
-	}
-
 	return nil
 }
 
@@ -1130,39 +1132,6 @@ func (nbs *NomsBlockStore) commit(ctx context.Context, current, last hash.Hash,
 		return true, nil
 	}
 
-	// check for dangling references in |nbs.mt|
-	if err = nbs.errorIfDangling(current, checker); err != nil {
-		if errors.Is(err, ErrDanglingRef) {
-			nbs.mt = nil
-		}
-		return false, err
-	}
-
-	// This is unfortunate. We want to serialize commits to the same store
-	// so that we avoid writing a bunch of unreachable small tables which result
-	// from optimistic lock failures. However, this means that the time to
-	// write tables is included in "commit" time and if all commits are
-	// serialized, it means a lot more waiting.
-	// "non-trivial" tables are persisted here, outside of the commit-lock.
-	// all other tables are persisted in updateManifest()
-	if nbs.mt != nil {
-		cnt, err := nbs.mt.count()
-		if err != nil {
-			return false, err
-		}
-
-		if cnt > preflushChunkCount {
-			ts, err := nbs.tables.append(ctx, nbs.mt, checker, nbs.hasCache, nbs.stats)
-			if err != nil {
-				if errors.Is(err, ErrDanglingRef) {
-					nbs.mt = nil
-				}
-				return false, err
-			}
-			nbs.tables, nbs.mt = ts, nil
-		}
-	}
-
 	nbs.mm.LockForUpdate()
 	defer func() {
 		unlockErr := nbs.mm.UnlockForUpdate()
@@ -1233,11 +1202,10 @@ func (nbs *NomsBlockStore) updateManifest(ctx context.Context, current, last has
 		if cnt > 0 {
 			ts, err := nbs.tables.append(ctx, nbs.mt, checker, nbs.hasCache, nbs.stats)
 			if err != nil {
-				if errors.Is(err, ErrDanglingRef) {
-					nbs.mt = nil
-				}
+				nbs.handlePossibleDanglingRefError(err)
 				return err
 			}
+			nbs.addPendingRefsToHasCache()
 			nbs.tables, nbs.mt = ts, nil
 		}
 	}
@@ -1250,6 +1218,12 @@ func (nbs *NomsBlockStore) updateManifest(ctx context.Context, current, last has
 		return errOptimisticLockFailedTables
 	}
 
+	// check for dangling reference to the new root
+	if err = nbs.errorIfDangling(current, checker); err != nil {
+		nbs.handlePossibleDanglingRefError(err)
+		return err
+	}
+
 	specs, err := nbs.tables.toSpecs()
 	if err != nil {
 		return err

go/store/nbs/table_set.go

@@ -302,10 +302,6 @@ func (ts tableSet) append(ctx context.Context, mt *memTable, checker refCheck, h
 		return tableSet{}, fmt.Errorf("%w: found dangling references to %s", ErrDanglingRef, absent.String())
 	}
 
-	for _, e := range mt.pendingRefs {
-		hasCache.Add(*e.a, struct{}{})
-	}
-
 	cs, err := ts.p.Persist(ctx, mt, ts, stats)
 	if err != nil {
 		return tableSet{}, err