influx_tsm: ignore series index and convert all points

A case (#5606) was found where a lot of data unexpectedly disappeared from a database
following a TSM conversion.

The proximate cause was an inconsistency between the root Bolt DB bucket list
and the meta data in the "series" bucket of the same shard. There were apparently valid
series in Bolt DB buckets that were no longer referenced by the meta data
in the "series" bucket - so-called orphaned series; since the conversion
process only iterated across the series found in the meta data, the conversion process
caused the orphaned series to be removed from the converted shards. This resulted in the
unexpected removal of data from the TSM shards that had previously been accessible
(despite the meta data inconsistency) in the b1 shards.

The root cause of the meta data inconsistency in the case above was a failure, in versions prior
to v0.9.3 (actually 3348dab) to update the "series" bucket with series that had been created in
previous shards during the life of the same influxd process instance.

This fix is required to avoid data loss during TSM conversions for shards that were created with
versions of influx that did not include 3348dab (e.g. prior to v0.9.3).

Analysis-by: Jon Seymour <jon@wildducktheories.com>

cmd/influx_tsm/b1/reader.go

@@ -15,6 +15,13 @@ const DefaultChunkSize = 1000
 
 var NoFieldsFiltered uint64
 
+var excludedBuckets = map[string]bool{
+	"fields": true,
+	"meta":   true,
+	"series": true,
+	"wal":    true,
+}
+
 // Reader is used to read all data from a b1 shard.
 type Reader struct {
 	path string
@@ -27,7 +34,6 @@ type Reader struct {
 	keyBuf    string
 	valuesBuf []tsm1.Value
 
-	series map[string]*tsdb.Series
 	fields map[string]*tsdb.MeasurementFields
 	codecs map[string]*tsdb.FieldCodec
 
@@ -38,7 +44,6 @@ type Reader struct {
 func NewReader(path string) *Reader {
 	return &Reader{
 		path:   path,
-		series: make(map[string]*tsdb.Series),
 		fields: make(map[string]*tsdb.MeasurementFields),
 		codecs: make(map[string]*tsdb.FieldCodec),
 	}
@@ -71,32 +76,31 @@ func (r *Reader) Open() error {
 		return err
 	}
 
-	// Load series
+	seriesSet := make(map[string]bool)
-	if err := r.db.View(func(tx *bolt.Tx) error {
-		meta := tx.Bucket([]byte("series"))
-		c := meta.Cursor()
 
-		for k, v := c.First(); k != nil; k, v = c.Next() {
+	// ignore series index and find all series in this shard
-			series := &tsdb.Series{}
+	if err := r.db.View(func(tx *bolt.Tx) error {
-			if err := series.UnmarshalBinary(v); err != nil {
+		tx.ForEach(func(name []byte, _ *bolt.Bucket) error {
-				return err
+			key := string(name)
+			if !excludedBuckets[key] {
+				seriesSet[key] = true
 			}
-			r.series[string(k)] = series
+			return nil
-		}
+		})
 		return nil
 	}); err != nil {
 		return err
 	}
 
-	// Create cursor for each field of each series.
 	r.tx, err = r.db.Begin(false)
 	if err != nil {
 		return err
 	}
 
-	for s := range r.series {
+	// Create cursor for each field of each series.
+	for s := range seriesSet {
 		measurement := tsdb.MeasurementFromSeriesKey(s)
-		fields := r.fields[tsdb.MeasurementFromSeriesKey(s)]
+		fields := r.fields[measurement]
 		if fields == nil {
 			atomic.AddUint64(&NoFieldsFiltered, 1)
 			continue

cmd/influx_tsm/bz1/reader.go

@@ -31,7 +31,6 @@ type Reader struct {
 	keyBuf    string
 	valuesBuf []tsm.Value
 
-	series map[string]*tsdb.Series
 	fields map[string]*tsdb.MeasurementFields
 	codecs map[string]*tsdb.FieldCodec
 
@@ -42,7 +41,6 @@ type Reader struct {
 func NewReader(path string) *Reader {
 	return &Reader{
 		path:      path,
-		series:    make(map[string]*tsdb.Series),
 		fields:    make(map[string]*tsdb.MeasurementFields),
 		codecs:    make(map[string]*tsdb.FieldCodec),
 		ChunkSize: DefaultChunkSize,
@@ -58,6 +56,8 @@ func (r *Reader) Open() error {
 	}
 	r.db = db
 
+	seriesSet := make(map[string]bool)
+
 	if err := r.db.View(func(tx *bolt.Tx) error {
 		var data []byte
 
@@ -66,20 +66,20 @@ func (r *Reader) Open() error {
 			// No data in this shard.
 			return nil
 		}
-		buf := meta.Get([]byte("series"))
+
-		if buf == nil {
+		pointsBucket := tx.Bucket([]byte("points"))
-			// No data in this shard.
+		if pointsBucket == nil {
 			return nil
 		}
-		data, err = snappy.Decode(nil, buf)
+
-		if err != nil {
+		if err := pointsBucket.ForEach(func(key, _ []byte) error {
-			return err
+			seriesSet[string(key)] = true
-		}
+			return nil
-		if err := json.Unmarshal(data, &r.series); err != nil {
+		}); err != nil {
 			return err
 		}
 
-		buf = meta.Get([]byte("fields"))
+		buf := meta.Get([]byte("fields"))
 		if buf == nil {
 			// No data in this shard.
 			return nil
@@ -102,15 +102,15 @@ func (r *Reader) Open() error {
 		r.codecs[k] = tsdb.NewFieldCodec(v.Fields)
 	}
 
-	// Create cursor for each field of each series.
 	r.tx, err = r.db.Begin(false)
 	if err != nil {
 		return err
 	}
 
-	for s := range r.series {
+	// Create cursor for each field of each series.
+	for s := range seriesSet {
 		measurement := tsdb.MeasurementFromSeriesKey(s)
-		fields := r.fields[tsdb.MeasurementFromSeriesKey(s)]
+		fields := r.fields[measurement]
 		if fields == nil {
 			atomic.AddUint64(&NoFieldsFiltered, 1)
 			continue

cmd/influx_tsm/main.go

@@ -42,7 +42,7 @@ The backed-up files must be removed manually, generally after starting up the
 node again to make sure all of data has been converted correctly.
 
 To restore a backup:
-  Shut down the node, remove the converted directory, and 
+  Shut down the node, remove the converted directory, and
   copy the backed-up directory to the original location.`
 
 type options struct {
@@ -54,7 +54,6 @@ type options struct {
 	Parallel       bool
 	SkipBackup     bool
 	UpdateInterval time.Duration
-	// Quiet          bool
 }
 
 func (o *options) Parse() error {
@@ -67,7 +66,6 @@ func (o *options) Parse() error {
 	fs.BoolVar(&opts.Parallel, "parallel", false, "Perform parallel conversion. (up to GOMAXPROCS shards at once)")
 	fs.BoolVar(&opts.SkipBackup, "nobackup", false, "Disable database backups. Not recommended.")
 	fs.StringVar(&opts.BackupPath, "backup", "", "The location to backup up the current databases. Must not be within the data directory.")
-	// fs.BoolVar(&opts.Quiet, "quiet", false, "Suppresses the regular status updates.")
 	fs.StringVar(&opts.DebugAddr, "debug", "", "If set, http debugging endpoints will be enabled on the given address")
 	fs.DurationVar(&opts.UpdateInterval, "interval", 5*time.Second, "How often status updates are printed.")
 	fs.Usage = func() {