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bolt db works

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This commit is contained in:
Barak Michener 2014-08-11 05:31:34 -04:00
parent d261e5d870
commit 82e4d122fc
5 changed files with 272 additions and 203 deletions
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133
graph/bolt/all_iterator.go
View file

@ -19,6 +19,9 @@ import (
"fmt"
"strings"
"github.com/barakmich/glog"
"github.com/boltdb/bolt"
"github.com/google/cayley/graph"
"github.com/google/cayley/graph/iterator"
"github.com/google/cayley/quad"
@ -27,34 +30,22 @@ import (
type AllIterator struct {
uid uint64
tags graph.Tagger
prefix []byte
bucket []byte
dir quad.Direction
open bool
qs *QuadStore
result graph.Value
result *Token
buffer [][]byte
offset int
done bool
}
func NewAllIterator(prefix string, d quad.Direction, ts *QuadStore) *AllIterator {
opts := &opt.ReadOptions{
DontFillCache: true,
}
func NewAllIterator(bucket []byte, d quad.Direction, qs *QuadStore) *AllIterator {
it := AllIterator{
uid: iterator.NextUID(),
ro: opts,
iter: ts.db.NewIterator(nil, opts),
prefix: []byte(prefix),
bucket: bucket,
dir: d,
open: true,
ts: ts,
}
it.iter.Seek(it.prefix)
if !it.iter.Valid() {
// FIXME(kortschak) What are the semantics here? Is this iterator usable?
// If not, we should return nil *Iterator and an error.
it.open = false
it.iter.Release()
qs: qs,
}
return &it
@ -65,15 +56,9 @@ func (it *AllIterator) UID() uint64 {
}
func (it *AllIterator) Reset() {
if !it.open {
it.iter = it.ts.db.NewIterator(nil, it.ro)
it.open = true
}
it.iter.Seek(it.prefix)
if !it.iter.Valid() {
it.open = false
it.iter.Release()
}
it.buffer = nil
it.offset = 0
it.done = false
}
func (it *AllIterator) Tagger() *graph.Tagger {
@ -91,28 +76,65 @@ func (it *AllIterator) TagResults(dst map[string]graph.Value) {
}
func (it *AllIterator) Clone() graph.Iterator {
out := NewAllIterator(string(it.prefix), it.dir, it.ts)
out := NewAllIterator(it.bucket, it.dir, it.qs)
out.tags.CopyFrom(it)
return out
}
func (it *AllIterator) Next() bool {
if !it.open {
it.result = nil
if it.done {
return false
}
var out []byte
out = make([]byte, len(it.iter.Key()))
copy(out, it.iter.Key())
it.iter.Next()
if !it.iter.Valid() {
it.Close()
if len(it.buffer) <= it.offset+1 {
it.offset = 0
var last []byte
if it.buffer != nil {
last = it.buffer[len(it.buffer)-1]
}
it.buffer = make([][]byte, 0, bufferSize)
err := it.qs.db.View(func(tx *bolt.Tx) error {
i := 0
b := tx.Bucket(it.bucket)
cur := b.Cursor()
if last == nil {
k, _ := cur.First()
var out []byte
out = make([]byte, len(k))
copy(out, k)
it.buffer = append(it.buffer, out)
i++
} else {
k, _ := cur.Seek(last)
if !bytes.Equal(k, last) {
return fmt.Errorf("Couldn't pick up after", k)
}
}
for i < bufferSize {
k, _ := cur.Next()
if k == nil {
it.buffer = append(it.buffer, k)
break
}
var out []byte
out = make([]byte, len(k))
copy(out, k)
it.buffer = append(it.buffer, out)
i++
}
return nil
})
if err != nil {
glog.Error("Error nexting in database: ", err)
it.done = true
return false
}
} else {
it.offset++
}
if !bytes.HasPrefix(out, it.prefix) {
it.Close()
if it.Result() == nil {
it.done = true
return false
}
it.result = Token(out)
return true
}
@ -121,7 +143,16 @@ func (it *AllIterator) ResultTree() *graph.ResultTree {
}
func (it *AllIterator) Result() graph.Value {
return it.result
if it.done {
return nil
}
if it.result != nil {
return it.result
}
if it.offset >= len(it.buffer) {
return nil
}
return &Token{bucket: it.bucket, key: it.buffer[it.offset]}
}
func (it *AllIterator) NextPath() bool {
@ -134,29 +165,23 @@ func (it *AllIterator) SubIterators() []graph.Iterator {
}
func (it *AllIterator) Contains(v graph.Value) bool {
it.result = v
it.result = v.(*Token)
return true
}
func (it *AllIterator) Close() {
if it.open {
it.iter.Release()
it.open = false
}
it.result = nil
it.buffer = nil
it.done = true
}
func (it *AllIterator) Size() (int64, bool) {
size, err := it.ts.SizeOfPrefix(it.prefix)
if err == nil {
return size, false
}
// INT64_MAX
return int64(^uint64(0) >> 1), false
return it.qs.size, true
}
func (it *AllIterator) DebugString(indent int) string {
size, _ := it.Size()
return fmt.Sprintf("%s(%s tags: %v leveldb size:%d %s %p)", strings.Repeat(" ", indent), it.Type(), it.tags.Tags(), size, it.dir, it)
return fmt.Sprintf("%s(%s tags: %v bolt size:%d %s %p)", strings.Repeat(" ", indent), it.Type(), it.tags.Tags(), size, it.dir, it)
}
func (it *AllIterator) Type() graph.Type { return graph.All }

247
graph/bolt/iterator.go
View file

@ -17,12 +17,12 @@ package bolt
import (
"bytes"
"encoding/json"
"errors"
"fmt"
"strings"
"github.com/barakmich/glog"
ldbit "github.com/syndtr/goleveldb/leveldb/iterator"
"github.com/syndtr/goleveldb/leveldb/opt"
"github.com/boltdb/bolt"
"github.com/google/cayley/graph"
"github.com/google/cayley/graph/iterator"
@ -30,48 +30,38 @@ import (
)
type Iterator struct {
uid uint64
tags graph.Tagger
nextPrefix []byte
checkId []byte
dir quad.Direction
open bool
iter ldbit.Iterator
qs *QuadStore
ro *opt.ReadOptions
originalPrefix string
result graph.Value
uid uint64
tags graph.Tagger
bucket []byte
checkId []byte
dir quad.Direction
qs *QuadStore
result *Token
buffer [][]byte
offset int
done bool
size int64
}
func NewIterator(prefix string, d quad.Direction, value graph.Value, qs *QuadStore) graph.Iterator {
vb := value.(Token)
p := make([]byte, 0, 2+qs.hasher.Size())
p = append(p, []byte(prefix)...)
p = append(p, []byte(vb[1:])...)
var bufferSize = 50
opts := &opt.ReadOptions{
DontFillCache: true,
func NewIterator(bucket []byte, d quad.Direction, value graph.Value, qs *QuadStore) graph.Iterator {
tok := value.(*Token)
if !bytes.Equal(tok.bucket, nodeBucket) {
glog.Error("Creating an iterator from a non-node value.")
return &iterator.Null{}
}
it := Iterator{
uid: iterator.NextUID(),
nextPrefix: p,
checkId: vb,
dir: d,
originalPrefix: prefix,
ro: opts,
iter: qs.db.NewIterator(nil, opts),
open: true,
qs: qs,
uid: iterator.NextUID(),
bucket: bucket,
dir: d,
qs: qs,
size: qs.SizeOf(value),
}
ok := it.iter.Seek(it.nextPrefix)
if !ok {
it.open = false
it.iter.Release()
glog.Error("Opening LevelDB iterator couldn't seek to location ", it.nextPrefix)
return &iterator.Null{}
}
it.checkId = make([]byte, len(tok.key))
copy(it.checkId, tok.key)
return &it
}
@ -81,15 +71,9 @@ func (it *Iterator) UID() uint64 {
}
func (it *Iterator) Reset() {
if !it.open {
it.iter = it.qs.db.NewIterator(nil, it.ro)
it.open = true
}
ok := it.iter.Seek(it.nextPrefix)
if !ok {
it.open = false
it.iter.Release()
}
it.buffer = nil
it.offset = 0
it.done = false
}
func (it *Iterator) Tagger() *graph.Tagger {
@ -107,16 +91,15 @@ func (it *Iterator) TagResults(dst map[string]graph.Value) {
}
func (it *Iterator) Clone() graph.Iterator {
out := NewIterator(it.originalPrefix, it.dir, Token(it.checkId), it.qs)
out := NewIterator(it.bucket, it.dir, &Token{nodeBucket, it.checkId}, it.qs)
out.Tagger().CopyFrom(it)
return out
}
func (it *Iterator) Close() {
if it.open {
it.iter.Release()
it.open = false
}
it.result = nil
it.buffer = nil
it.done = true
}
func (it *Iterator) isLiveValue(val []byte) bool {
@ -125,36 +108,73 @@ func (it *Iterator) isLiveValue(val []byte) bool {
return len(entry.History)%2 != 0
}
var errNotExist = errors.New("Triple doesn't exist")
func (it *Iterator) Next() bool {
if it.iter == nil {
it.result = nil
if it.done {
return false
}
if !it.open {
it.result = nil
return false
}
if !it.iter.Valid() {
it.result = nil
it.Close()
return false
}
if bytes.HasPrefix(it.iter.Key(), it.nextPrefix) {
if !it.isLiveValue(it.iter.Value()) {
return it.Next()
if len(it.buffer) <= it.offset+1 {
it.offset = 0
var last []byte
if it.buffer != nil {
last = it.buffer[len(it.buffer)-1]
}
out := make([]byte, len(it.iter.Key()))
copy(out, it.iter.Key())
it.result = Token(out)
ok := it.iter.Next()
if !ok {
it.Close()
it.buffer = make([][]byte, 0, bufferSize)
err := it.qs.db.View(func(tx *bolt.Tx) error {
i := 0
b := tx.Bucket(it.bucket)
cur := b.Cursor()
if last == nil {
k, _ := cur.Seek(it.checkId)
if bytes.HasPrefix(k, it.checkId) {
var out []byte
out = make([]byte, len(k))
copy(out, k)
it.buffer = append(it.buffer, out)
i++
} else {
it.buffer = append(it.buffer, nil)
return errNotExist
}
} else {
k, _ := cur.Seek(last)
if !bytes.Equal(k, last) {
return fmt.Errorf("Couldn't pick up after", k)
}
}
for i < bufferSize {
k, v := cur.Next()
if k == nil || !bytes.HasPrefix(k, it.checkId) {
it.buffer = append(it.buffer, nil)
break
}
if !it.isLiveValue(v) {
continue
}
var out []byte
out = make([]byte, len(k))
copy(out, k)
it.buffer = append(it.buffer, out)
i++
}
return nil
})
if err != nil {
if err != errNotExist {
glog.Error("Error nexting in database: ", err)
}
it.done = true
return false
}
return true
} else {
it.offset++
}
it.Close()
it.result = nil
return false
if it.Result() == nil {
it.done = true
return false
}
return true
}
func (it *Iterator) ResultTree() *graph.ResultTree {
@ -162,7 +182,19 @@ func (it *Iterator) ResultTree() *graph.ResultTree {
}
func (it *Iterator) Result() graph.Value {
return it.result
if it.done {
return nil
}
if it.result != nil {
return it.result
}
if it.offset >= len(it.buffer) {
return nil
}
if it.buffer[it.offset] == nil {
return nil
}
return &Token{bucket: it.bucket, key: it.buffer[it.offset]}
}
func (it *Iterator) NextPath() bool {
@ -174,65 +206,65 @@ func (it *Iterator) SubIterators() []graph.Iterator {
return nil
}
func PositionOf(prefix []byte, d quad.Direction, qs *QuadStore) int {
if bytes.Equal(prefix, []byte("sp")) {
func PositionOf(tok *Token, d quad.Direction, qs *QuadStore) int {
if bytes.Equal(tok.bucket, spoBucket) {
switch d {
case quad.Subject:
return 2
return 0
case quad.Predicate:
return qs.hasher.Size() + 2
return qs.hasher.Size()
case quad.Object:
return 2*qs.hasher.Size() + 2
return 2 * qs.hasher.Size()
case quad.Label:
return 3*qs.hasher.Size() + 2
return 3 * qs.hasher.Size()
}
}
if bytes.Equal(prefix, []byte("po")) {
if bytes.Equal(tok.bucket, posBucket) {
switch d {
case quad.Subject:
return 2*qs.hasher.Size() + 2
return 2 * qs.hasher.Size()
case quad.Predicate:
return 2
return 0
case quad.Object:
return qs.hasher.Size() + 2
return qs.hasher.Size()
case quad.Label:
return 3*qs.hasher.Size() + 2
return 3 * qs.hasher.Size()
}
}
if bytes.Equal(prefix, []byte("os")) {
if bytes.Equal(tok.bucket, ospBucket) {
switch d {
case quad.Subject:
return qs.hasher.Size() + 2
return qs.hasher.Size()
case quad.Predicate:
return 2*qs.hasher.Size() + 2
return 2 * qs.hasher.Size()
case quad.Object:
return 2
return 0
case quad.Label:
return 3*qs.hasher.Size() + 2
return 3 * qs.hasher.Size()
}
}
if bytes.Equal(prefix, []byte("cp")) {
if bytes.Equal(tok.bucket, cpsBucket) {
switch d {
case quad.Subject:
return 2*qs.hasher.Size() + 2
return 2 * qs.hasher.Size()
case quad.Predicate:
return qs.hasher.Size() + 2
return qs.hasher.Size()
case quad.Object:
return 3*qs.hasher.Size() + 2
return 3 * qs.hasher.Size()
case quad.Label:
return 2
return 0
}
}
panic("unreachable")
}
func (it *Iterator) Contains(v graph.Value) bool {
val := v.(Token)
if val[0] == 'z' {
val := v.(*Token)
if bytes.Equal(val.bucket, nodeBucket) {
return false
}
offset := PositionOf(val[0:2], it.dir, it.qs)
if bytes.HasPrefix(val[offset:], it.checkId[1:]) {
offset := PositionOf(val, it.dir, it.qs)
if bytes.HasPrefix(val.key[offset:], it.checkId) {
// You may ask, why don't we check to see if it's a valid (not deleted) triple
// again?
//
@ -248,31 +280,30 @@ func (it *Iterator) Contains(v graph.Value) bool {
}
func (it *Iterator) Size() (int64, bool) {
return it.qs.SizeOf(Token(it.checkId)), true
return it.size, true
}
func (it *Iterator) DebugString(indent int) string {
size, _ := it.Size()
return fmt.Sprintf("%s(%s %d tags: %v dir: %s size:%d %s)",
strings.Repeat(" ", indent),
it.Type(),
it.UID(),
it.tags.Tags(),
it.dir,
size,
it.qs.NameOf(Token(it.checkId)),
it.size,
it.qs.NameOf(&Token{it.bucket, it.checkId}),
)
}
var levelDBType graph.Type
var boltType graph.Type
func init() {
levelDBType = graph.RegisterIterator("leveldb")
boltType = graph.RegisterIterator("bolt")
}
func Type() graph.Type { return levelDBType }
func Type() graph.Type { return boltType }
func (it *Iterator) Type() graph.Type { return levelDBType }
func (it *Iterator) Type() graph.Type { return boltType }
func (it *Iterator) Sorted() bool { return false }
func (it *Iterator) Optimize() (graph.Iterator, bool) {

85
graph/bolt/quadstore.go
View file

@ -21,9 +21,11 @@ import (
"encoding/json"
"fmt"
"hash"
"time"
"github.com/barakmich/glog"
"github.com/boltdb/bolt"
"github.com/boltdb/coalescer"
"github.com/google/cayley/graph"
"github.com/google/cayley/graph/iterator"
@ -31,7 +33,7 @@ import (
)
func init() {
graph.RegisterTripleStore("bolt", true, newQuadStore, createNewLevelDB)
graph.RegisterTripleStore("bolt", true, newQuadStore, createNewBolt)
}
type Token struct {
@ -40,7 +42,7 @@ type Token struct {
}
func (t *Token) Key() interface{} {
return fmt.Sprint(t.bucket, t.data)
return fmt.Sprint(t.bucket, t.key)
}
type QuadStore struct {
@ -53,7 +55,6 @@ type QuadStore struct {
}
func createNewBolt(path string, _ graph.Options) error {
opts := &opt.Options{}
db, err := bolt.Open(path, 0600, nil)
if err != nil {
glog.Errorf("Error: couldn't create Bolt database: %v", err)
@ -62,9 +63,6 @@ func createNewBolt(path string, _ graph.Options) error {
defer db.Close()
qs := &QuadStore{}
qs.db = db
qs.writeopts = &opt.WriteOptions{
Sync: true,
}
err = qs.createBuckets()
if err != nil {
return err
@ -91,10 +89,10 @@ func newQuadStore(path string, options graph.Options) (graph.TripleStore, error)
}
func (qs *QuadStore) createBuckets() error {
return db.Update(func(tx *bolt.Tx) error {
return qs.db.Update(func(tx *bolt.Tx) error {
var err error
for _, bucket := range [][]byte{spo, osp, pos, cps} {
_, err = tx.CreateBucket(bucketFor(bucket))
for _, index := range [][4]quad.Direction{spo, osp, pos, cps} {
_, err = tx.CreateBucket(bucketFor(index))
if err != nil {
return fmt.Errorf("Couldn't create bucket: %s", err)
}
@ -111,6 +109,7 @@ func (qs *QuadStore) createBuckets() error {
if err != nil {
return fmt.Errorf("Couldn't create bucket: %s", err)
}
return nil
})
}
@ -152,10 +151,14 @@ type IndexEntry struct {
// Short hand for direction permutations.
var (
spo = bucketFor([4]quad.Direction{quad.Subject, quad.Predicate, quad.Object, quad.Label})
osp = bucketFor([4]quad.Direction{quad.Object, quad.Subject, quad.Predicate, quad.Label})
pos = bucketFor([4]quad.Direction{quad.Predicate, quad.Object, quad.Subject, quad.Label})
cps = bucketFor([4]quad.Direction{quad.Label, quad.Predicate, quad.Subject, quad.Object})
spo = [4]quad.Direction{quad.Subject, quad.Predicate, quad.Object, quad.Label}
osp = [4]quad.Direction{quad.Object, quad.Subject, quad.Predicate, quad.Label}
pos = [4]quad.Direction{quad.Predicate, quad.Object, quad.Subject, quad.Label}
cps = [4]quad.Direction{quad.Label, quad.Predicate, quad.Subject, quad.Object}
spoBucket = bucketFor(spo)
ospBucket = bucketFor(osp)
posBucket = bucketFor(pos)
cpsBucket = bucketFor(cps)
)
var logBucket = []byte("log")
@ -163,12 +166,14 @@ var nodeBucket = []byte("node")
var metaBucket = []byte("meta")
func (qs *QuadStore) ApplyDeltas(deltas []*graph.Delta) error {
batch := &leveldb.Batch{}
var size_change int64
var new_horizon int64
err := qs.db.Update(func(tx *bolt.Tx) error {
c, err := coalescer.New(qs.db, 200, 100*time.Millisecond)
if err != nil {
return err
}
err = c.Update(func(tx *bolt.Tx) error {
var b *bolt.Bucket
var err error
resizeMap := make(map[string]int64)
size_change = int64(0)
for _, d := range deltas {
@ -220,12 +225,11 @@ func (qs *QuadStore) ApplyDeltas(deltas []*graph.Delta) error {
func (qs *QuadStore) buildQuadWrite(tx *bolt.Tx, q quad.Quad, id int64, isAdd bool) error {
var entry IndexEntry
b := tx.Bucket(bucketFor(spo))
b := tx.Bucket(spoBucket)
data := b.Get(qs.createKeyFor(spo, q))
if data != nil {
// We got something.
err = json.Unmarshal(data, &entry)
err := json.Unmarshal(data, &entry)
if err != nil {
return err
}
@ -244,17 +248,17 @@ func (qs *QuadStore) buildQuadWrite(tx *bolt.Tx, q quad.Quad, id int64, isAdd bo
entry.History = append(entry.History, id)
bytes, err := json.Marshal(entry)
jsonbytes, err := json.Marshal(entry)
if err != nil {
glog.Errorf("Couldn't write to buffer for entry %#v: %s", entry, err)
return err
}
for _, bucket := range [][4]quad.Direction{spo, osp, pos, cps} {
if bucket == cps && q.Get(quad.Label) == "" {
for _, index := range [][4]quad.Direction{spo, osp, pos, cps} {
if index == cps && q.Get(quad.Label) == "" {
continue
}
b := tx.Bucket(bucketFor(bucket))
err = b.Put(qs.createKeyFor(bucket, q), bytes)
b := tx.Bucket(bucketFor(index))
err = b.Put(qs.createKeyFor(index, q), jsonbytes)
if err != nil {
return err
}
@ -268,14 +272,14 @@ type ValueData struct {
}
func (qs *QuadStore) UpdateValueKeyBy(name string, amount int64, tx *bolt.Tx) error {
value := &ValueData{name, amount}
value := ValueData{name, amount}
b := tx.Bucket(nodeBucket)
key := qs.createValueKeyFor(name)
data := b.Get(key)
if data != nil {
// Node exists in the database -- unmarshal and update.
err = json.Unmarshal(b, value)
err := json.Unmarshal(data, &value)
if err != nil {
glog.Errorf("Error: couldn't reconstruct value: %v", err)
return err
@ -336,13 +340,12 @@ func (qs *QuadStore) Quad(k graph.Value) quad.Quad {
tok := k.(*Token)
err := qs.db.View(func(tx *bolt.Tx) error {
b := tx.Bucket(tok.bucket)
data := qs.db.Get(tok.key, qs.readopts)
data := b.Get(tok.key)
if data == nil {
// No harm, no foul.
return nil
}
err = json.Unmarshal(data, &q)
return err
return json.Unmarshal(data, &q)
})
if err != nil {
glog.Error("Error getting triple: ", err)
@ -409,7 +412,7 @@ func (qs *QuadStore) getInt64ForKey(tx *bolt.Tx, key string, empty int64) (int64
return empty, nil
}
buf := bytes.NewBuffer(data)
err = binary.Read(buf, binary.LittleEndian, &out)
err := binary.Read(buf, binary.LittleEndian, &out)
if err != nil {
return 0, err
}
@ -419,31 +422,31 @@ func (qs *QuadStore) getInt64ForKey(tx *bolt.Tx, key string, empty int64) (int64
func (qs *QuadStore) getMetadata() error {
err := qs.db.View(func(tx *bolt.Tx) error {
var err error
qs.size, err = qs.getInt64ForKey("size", 0)
qs.size, err = qs.getInt64ForKey(tx, "size", 0)
if err != nil {
return err
}
qs.horizon, err = qs.getInt64ForKey("horizon", 0)
qs.horizon, err = qs.getInt64ForKey(tx, "horizon", 0)
return err
})
return err
}
func (qs *QuadStore) TripleIterator(d quad.Direction, val graph.Value) graph.Iterator {
var prefix []byte
var bucket []byte
switch d {
case quad.Subject:
prefix = spo
bucket = spoBucket
case quad.Predicate:
prefix = pos
bucket = posBucket
case quad.Object:
prefix = osp
bucket = ospBucket
case quad.Label:
prefix = cps
bucket = cpsBucket
default:
panic("unreachable " + d.String())
}
return NewIterator(prefix, d, val, qs)
return NewIterator(bucket, d, val, qs)
}
func (qs *QuadStore) NodesAllIterator() graph.Iterator {
@ -451,7 +454,7 @@ func (qs *QuadStore) NodesAllIterator() graph.Iterator {
}
func (qs *QuadStore) TriplesAllIterator() graph.Iterator {
return NewAllIterator(pos, quad.Predicate, qs)
return NewAllIterator(posBucket, quad.Predicate, qs)
}
func (qs *QuadStore) TripleDirection(val graph.Value, d quad.Direction) graph.Value {
@ -460,7 +463,7 @@ func (qs *QuadStore) TripleDirection(val graph.Value, d quad.Direction) graph.Va
if offset != -1 {
return &Token{
bucket: nodeBucket,
key: v[offset : offset+qs.hasher.Size()],
key: v.key[offset : offset+qs.hasher.Size()],
}
} else {
return qs.ValueOf(qs.Quad(v).Get(d))
@ -470,7 +473,7 @@ func (qs *QuadStore) TripleDirection(val graph.Value, d quad.Direction) graph.Va
func compareTokens(a, b graph.Value) bool {
atok := a.(*Token)
btok := b.(*Token)
return bytes.Equal(atok.key, btok.key) && atok.bucket == btok.bucket
return bytes.Equal(atok.key, btok.key) && bytes.Equal(atok.bucket, btok.bucket)
}
func (qs *QuadStore) FixedIterator() graph.FixedIterator {