// Returns all (z, y, x0, x1) Spans in sorted order: z, then y, then x0.
func getSpans(ctx storage.VersionedCtx, minIndex, maxIndex indexRLE) ([]dvid.Span, error) {
db, err := storage.SmallDataStore()
if err != nil {
return nil, err
}
spans := []dvid.Span{}
var f storage.ChunkFunc = func(chunk *storage.Chunk) error {
ibytes, err := chunk.K.ClassBytes(keyROI)
if err != nil {
return err
}
index := new(indexRLE)
if err = index.IndexFromBytes(ibytes); err != nil {
return fmt.Errorf("Unable to get indexRLE out of []byte encoding: %v\n", err)
}
z := index.start.Value(2)
y := index.start.Value(1)
x0 := index.start.Value(0)
x1 := x0 + int32(index.span) - 1
spans = append(spans, dvid.Span{z, y, x0, x1})
return nil
}
mintk := storage.NewTKey(keyROI, minIndex.Bytes())
maxtk := storage.NewTKey(keyROI, maxIndex.Bytes())
err = db.ProcessRange(ctx, mintk, maxtk, &storage.ChunkOp{}, f)
return spans, err
}
// NewTKey returns a TKey for storing a "label + spatial index", where
// the spatial index references a block that contains a voxel with the given label.
func NewTKey(label uint64, block dvid.IZYXString) storage.TKey {
sz := len(block)
ibytes := make([]byte, 8+sz)
binary.BigEndian.PutUint64(ibytes[0:8], label)
copy(ibytes[8:], []byte(block))
return storage.NewTKey(keyLabelBlockRLE, ibytes)
}
// NewTagTKey returns a TKey for a given tag.
func NewTagTKey(tag Tag) (storage.TKey, error) {
// Make sure the key has no embedded 0 values
for i := 0; i < len(tag); i++ {
if tag[i] == 0 {
return nil, fmt.Errorf("tag cannot have embedded 0 value")
}
}
return storage.NewTKey(keyTag, append([]byte(tag), 0)), nil
}
func (m *repoManager) putData(t storage.TKeyClass, data interface{}) error {
var ctx storage.MetadataContext
var buf bytes.Buffer
enc := gob.NewEncoder(&buf)
if err := enc.Encode(data); err != nil {
return err
}
return m.store.Put(ctx, storage.NewTKey(t, nil), buf.Bytes())
}
// NewTKey returns the "key" key component.
func NewTKey(key string) (storage.TKey, error) {
// Make sure the key has no embedded 0 values
for i := 0; i < len(key); i++ {
if key[i] == 0 {
return nil, fmt.Errorf("key cannot have embedded 0 value")
}
}
return storage.NewTKey(keyStandard, append([]byte(key), 0)), nil
}
// NewTypeSizeLabelTKey returns a type-specific key for the (index type, size, label) tuple.
func NewTypeSizeLabelTKey(i IndexType, sz uint32, label uint64) storage.TKey {
// Since we want biggest -> smallest sort and initially only have forward range queries,
// modify size to make smallest <-> largest.
rsz := math.MaxUint32 - sz
buf := make([]byte, 8+1+4)
buf[0] = byte(i)
binary.BigEndian.PutUint32(buf[1:5], rsz)
binary.BigEndian.PutUint64(buf[5:], label)
return storage.NewTKey(keyTypeSizeLabel, buf)
}
func (r *repoT) save() error {
compression, err := dvid.NewCompression(dvid.LZ4, dvid.DefaultCompression)
if err != nil {
return err
}
serialization, err := dvid.Serialize(r, compression, dvid.CRC32)
if err != nil {
return err
}
var ctx storage.MetadataContext
return manager.store.Put(ctx, storage.NewTKey(repoKey, r.id.Bytes()), serialization)
}
func (m *repoManager) loadData(t storage.TKeyClass, data interface{}) (found bool, err error) {
var ctx storage.MetadataContext
value, err := m.store.Get(ctx, storage.NewTKey(t, nil))
if err != nil {
return false, fmt.Errorf("Bad metadata GET: %v", err)
}
if value == nil {
return false, nil
}
buf := bytes.NewBuffer(value)
dec := gob.NewDecoder(buf)
if err := dec.Decode(data); err != nil {
return false, fmt.Errorf("Could not decode Gob encoded metadata (len %d): %v", len(value), err)
}
return true, nil
}
// Load the next ids to be used for RepoID, VersionID, and InstanceID.
func (m *repoManager) loadNewIDs() error {
var ctx storage.MetadataContext
value, err := m.store.Get(ctx, storage.NewTKey(newIDsKey, nil))
if err != nil {
return err
}
if len(value) != dvid.RepoIDSize+dvid.VersionIDSize+dvid.InstanceIDSize {
return fmt.Errorf("Bad value returned for new ids. Length %d bytes!", len(value))
}
pos := 0
m.repoID = dvid.RepoIDFromBytes(value[pos : pos+dvid.RepoIDSize])
pos += dvid.RepoIDSize
m.versionID = dvid.VersionIDFromBytes(value[pos : pos+dvid.VersionIDSize])
pos += dvid.VersionIDSize
m.instanceID = dvid.InstanceIDFromBytes(value[pos : pos+dvid.InstanceIDSize])
return nil
}
keyRepoLabelMax = 229
)
// NewTKey returns a TKey for storing a "label + spatial index", where
// the spatial index references a block that contains a voxel with the given label.
func NewTKey(label uint64, block dvid.IZYXString) storage.TKey {
sz := len(block)
ibytes := make([]byte, 8+sz)
binary.BigEndian.PutUint64(ibytes[0:8], label)
copy(ibytes[8:], []byte(block))
return storage.NewTKey(keyLabelBlockRLE, ibytes)
}
// DecodeTKey returns a label and block index bytes from a label block RLE key.
// The block index bytes are returned because different block indices may be used (e.g., CZYX),
// and its up to caller to determine which one is used for this particular key.
func DecodeTKey(tk storage.TKey) (label uint64, block dvid.IZYXString, err error) {
ibytes, err := tk.ClassBytes(keyLabelBlockRLE)
if err != nil {
return
}
label = binary.BigEndian.Uint64(ibytes[0:8])
block = dvid.IZYXString(ibytes[8:])
return
}
var (
maxLabelTKey = storage.NewTKey(keyLabelMax, nil)
maxRepoLabelTKey = storage.NewTKey(keyRepoLabelMax, nil)
)
// PutSpans saves a slice of spans representing an ROI into the datastore.
// If the init parameter is true, all previous spans of this ROI are deleted before
// writing these spans.
func (d *Data) PutSpans(versionID dvid.VersionID, spans []dvid.Span, init bool) error {
ctx := datastore.NewVersionedCtx(d, versionID)
db, err := storage.SmallDataStore()
if err != nil {
return err
}
// Delete the old key/values
if init {
if err := d.Delete(ctx); err != nil {
return err
}
}
// Make sure our small data store can do batching.
batcher, ok := db.(storage.KeyValueBatcher)
if !ok {
return fmt.Errorf("Unable to store ROI: small data store can't do batching!")
}
// We only want one PUT on given version for given data to prevent interleaved PUTs.
putMutex := ctx.Mutex()
putMutex.Lock()
// Save new extents after finished.
defer func() {
err := datastore.SaveDataByVersion(ctx.VersionID(), d)
if err != nil {
dvid.Errorf("Error in trying to save repo on roi extent change: %v\n", err)
}
putMutex.Unlock()
}()
// Put the new key/values
const BATCH_SIZE = 10000
batch := batcher.NewBatch(ctx)
for i, span := range spans {
if span[0] < d.MinZ {
d.MinZ = span[0]
}
if span[0] > d.MaxZ {
d.MaxZ = span[0]
}
if span[3] < span[2] {
return fmt.Errorf("Got weird span %v. span[3] (X1) < span[2] (X0)", span)
}
index := indexRLE{
start: dvid.IndexZYX{span[2], span[1], span[0]},
span: uint32(span[3] - span[2] + 1),
}
tk := storage.NewTKey(keyROI, index.Bytes())
batch.Put(tk, dvid.EmptyValue())
if (i+1)%BATCH_SIZE == 0 {
if err := batch.Commit(); err != nil {
return fmt.Errorf("Error on batch PUT at span %d: %v\n", i, err)
}
batch = batcher.NewBatch(ctx)
}
}
if len(spans)%BATCH_SIZE != 0 {
if err := batch.Commit(); err != nil {
return fmt.Errorf("Error on last batch PUT: %v\n", err)
}
}
return nil
}
// deletes a Repo from the datastore
func (r *repoT) delete() error {
var ctx storage.MetadataContext
tkey := storage.NewTKey(repoKey, r.id.Bytes())
return manager.store.Delete(ctx, tkey)
}
func NewLabelTKey(label uint64) storage.TKey {
buf := make([]byte, 8)
binary.BigEndian.PutUint64(buf, label)
return storage.NewTKey(keyLabel, buf)
}
// NewTypeLabelTKey returns a type-specific key for the (index type, label) tuple.
func NewTypeLabelTKey(i IndexType, label uint64) storage.TKey {
buf := make([]byte, 1+8)
buf[0] = byte(i)
binary.BigEndian.PutUint64(buf[1:], label)
return storage.NewTKey(keyTypeLabel, buf)
}
func NewBlockTKey(pt dvid.ChunkPoint3d) storage.TKey {
idx := dvid.IndexZYX(pt)
return storage.NewTKey(keyBlock, idx.Bytes())
}
// NewSizeLabelTKey returns a key component for storing a "size + label".
func NewSizeLabelTKey(size, label uint64) storage.TKey {
ibytes := make([]byte, 16)
binary.BigEndian.PutUint64(ibytes[0:8], size)
binary.BigEndian.PutUint64(ibytes[8:16], label)
return storage.NewTKey(keySizeLabel, ibytes)
}
// NewTKeyByCoord returns a TKey for a block coord in string format.
func NewTKeyByCoord(izyx dvid.IZYXString) storage.TKey {
return storage.NewTKey(keyImageBlock, []byte(izyx))
}
// no checking of key
func newTKey(key string) storage.TKey {
return storage.NewTKey(keyStandard, append([]byte(key), 0))
}
func (m *repoManager) putNewIDs() error {
var ctx storage.MetadataContext
value := append(m.repoID.Bytes(), m.versionID.Bytes()...)
value = append(value, m.instanceID.Bytes()...)
return m.store.Put(ctx, storage.NewTKey(newIDsKey, nil), value)
}
// NewLabelSizeTKey returns a key component for a "label + size".
func NewLabelSizeTKey(label, size uint64) storage.TKey {
ibytes := make([]byte, 16)
binary.BigEndian.PutUint64(ibytes[0:8], label)
binary.BigEndian.PutUint64(ibytes[8:16], size)
return storage.NewTKey(keyLabelSize, ibytes)
}
func (m *repoManager) loadVersion0() error {
// Load the maps
if _, err := m.loadData(repoToUUIDKey, &(m.repoToUUID)); err != nil {
return fmt.Errorf("Error loading repo to UUID map: %s", err)
}
if _, err := m.loadData(versionToUUIDKey, &(m.versionToUUID)); err != nil {
return fmt.Errorf("Error loading version to UUID map: %s", err)
}
if err := m.loadNewIDs(); err != nil {
return fmt.Errorf("Error loading new local ids: %s", err)
}
// Generate the inverse UUID to VersionID mapping.
for v, uuid := range m.versionToUUID {
m.uuidToVersion[uuid] = v
}
// Load all the repo data
var ctx storage.MetadataContext
minRepo := dvid.RepoID(0)
maxRepo := dvid.RepoID(dvid.MaxRepoID)
minTKey := storage.NewTKey(repoKey, minRepo.Bytes())
maxTKey := storage.NewTKey(repoKey, maxRepo.Bytes())
kvList, err := m.store.GetRange(ctx, minTKey, maxTKey)
if err != nil {
return err
}
var saveCache bool
for _, kv := range kvList {
var saveRepo bool
ibytes, err := kv.K.ClassBytes(repoKey)
if err != nil {
return err
}
repoID := dvid.RepoIDFromBytes(ibytes)
// Load each repo
_, found := m.repoToUUID[repoID]
if !found {
return fmt.Errorf("Retrieved repo with id %d that is not in map. Corrupt DB?", repoID)
}
r := &repoT{
log: []string{},
properties: make(map[string]interface{}),
data: make(map[dvid.InstanceName]DataService),
}
if err = dvid.Deserialize(kv.V, r); err != nil {
return fmt.Errorf("Error gob decoding repo %d: %v", repoID, err)
}
// Cache all UUID from nodes into our high-level cache
for v, node := range r.dag.nodes {
uuid, found := m.versionToUUID[v]
if !found {
dvid.Errorf("Version id %d found in repo %s (id %d) not in cache map. Adding it...", v, r.uuid, r.id)
m.versionToUUID[v] = node.uuid
m.uuidToVersion[node.uuid] = v
uuid = node.uuid
saveCache = true
}
m.repos[uuid] = r
}
// Populate the instance id -> dataservice map.
for _, dataservice := range r.data {
m.iids[dataservice.InstanceID()] = dataservice
}
// Update the sync graph with all syncable data instances in this repo
for _, dataservice := range r.data {
syncedData, syncable := dataservice.(Syncer)
if syncable {
for _, name := range syncedData.SyncedNames() {
r.addSyncGraph(syncedData.InitSync(name))
}
}
}
// Load any mutable properties for the data instances.
for _, dataservice := range r.data {
mutator, mutable := dataservice.(InstanceMutator)
if mutable {
saveRepo, err = mutator.LoadMutable(r.version, m.formatVersion, RepoFormatVersion)
if err != nil {
return err
}
}
}
// If updates had to be made, save the migrated repo metadata.
if saveRepo {
dvid.Infof("Re-saved repo with root %s due to migrations.\n", r.uuid)
if err := r.save(); err != nil {
return err
}
}
}
if err := m.verifyCompiledTypes(); err != nil {
return err
}
// If we noticed missing cache entries, save current metadata.
if saveCache {
if err := m.putCaches(); err != nil {
return err
}
}
if m.formatVersion != RepoFormatVersion {
dvid.Infof("Updated metadata from version %d to version %d\n", m.formatVersion, RepoFormatVersion)
m.formatVersion = RepoFormatVersion
if err := m.putData(formatKey, &(m.formatVersion)); err != nil {
return err
}
}
dvid.Infof("Loaded %d repositories from metadata store.", len(m.repos))
return nil
}
// NewTKey returns the "key" key component.
func NewTKey(key string) (storage.TKey, error) {
return storage.NewTKey(keyStandard, append([]byte(key), 0)), nil
}