fix: recreate index include deleted files (#5579)

* fix: recreate index include deleted files
https://github.com/seaweedfs/seaweedfs/issues/5508

* fix: counting the number of files

* fix: log

weed/command/fix.go

@@ -32,12 +32,15 @@ var cmdFix = &Command{
 var (
 	fixVolumeCollection = cmdFix.Flag.String("collection", "", "an optional volume collection name, if specified only it will be processed")
 	fixVolumeId         = cmdFix.Flag.Int64("volumeId", 0, "an optional volume id, if not 0 (default) only it will be processed")
+	fixIncludeDeleted   = cmdFix.Flag.Bool("includeDeleted", true, "include deleted entries in the index file")
 	fixIgnoreError      = cmdFix.Flag.Bool("ignoreError", false, "an optional, if true will be processed despite errors")
 )
 
 type VolumeFileScanner4Fix struct {
-	version needle.Version
+	version        needle.Version
-	nm      *needle_map.MemDb
+	nm             *needle_map.MemDb
+	nmDeleted      *needle_map.MemDb
+	includeDeleted bool
 }
 
 func (scanner *VolumeFileScanner4Fix) VisitSuperBlock(superBlock super_block.SuperBlock) error {
@@ -50,13 +53,20 @@ func (scanner *VolumeFileScanner4Fix) ReadNeedleBody() bool {
 }
 
 func (scanner *VolumeFileScanner4Fix) VisitNeedle(n *needle.Needle, offset int64, needleHeader, needleBody []byte) error {
-	glog.V(2).Infof("key %d offset %d size %d disk_size %d compressed %v", n.Id, offset, n.Size, n.DiskSize(scanner.version), n.IsCompressed())
+	glog.V(2).Infof("key %v offset %d size %d disk_size %d compressed %v", n.Id, offset, n.Size, n.DiskSize(scanner.version), n.IsCompressed())
 	if n.Size.IsValid() {
-		pe := scanner.nm.Set(n.Id, types.ToOffset(offset), n.Size)
+		if pe := scanner.nm.Set(n.Id, types.ToOffset(offset), n.Size); pe != nil {
-		glog.V(2).Infof("saved %d with error %v", n.Size, pe)
+			return fmt.Errorf("saved %d with error %v", n.Size, pe)
+		}
 	} else {
-		glog.V(2).Infof("skipping deleted file ...")
+		if scanner.includeDeleted {
-		return scanner.nm.Delete(n.Id)
+			if pe := scanner.nmDeleted.Set(n.Id, types.ToOffset(offset), types.TombstoneFileSize); pe != nil {
+				return fmt.Errorf("saved deleted %d with error %v", n.Size, pe)
+			}
+		} else {
+			glog.V(2).Infof("skipping deleted file ...")
+			return scanner.nm.Delete(n.Id)
+		}
 	}
 	return nil
 }
@@ -109,21 +119,45 @@ func runFix(cmd *Command, args []string) bool {
 			if *fixVolumeId != 0 && *fixVolumeId != volumeId {
 				continue
 			}
-			doFixOneVolume(basePath, baseFileName, collection, volumeId)
+			doFixOneVolume(basePath, baseFileName, collection, volumeId, *fixIncludeDeleted)
 		}
 	}
 	return true
 }
 
-func doFixOneVolume(basepath string, baseFileName string, collection string, volumeId int64) {
+func SaveToIdx(scaner *VolumeFileScanner4Fix, idxName string) (ret error) {
+	idxFile, err := os.OpenFile(idxName, os.O_WRONLY|os.O_CREATE|os.O_TRUNC, 0644)
+	if err != nil {
+		return
+	}
+	defer func() {
+		idxFile.Close()
+	}()
+
+	return scaner.nm.AscendingVisit(func(value needle_map.NeedleValue) error {
+		_, err := idxFile.Write(value.ToBytes())
+		if scaner.includeDeleted && err == nil {
+			if deleted, ok := scaner.nmDeleted.Get(value.Key); ok {
+				_, err = idxFile.Write(deleted.ToBytes())
+			}
+		}
+		return err
+	})
+}
+
+func doFixOneVolume(basepath string, baseFileName string, collection string, volumeId int64, fixIncludeDeleted bool) {
 	indexFileName := path.Join(basepath, baseFileName+".idx")
 
 	nm := needle_map.NewMemDb()
+	nmDeleted := needle_map.NewMemDb()
 	defer nm.Close()
+	defer nmDeleted.Close()
 
 	vid := needle.VolumeId(volumeId)
 	scanner := &VolumeFileScanner4Fix{
-		nm: nm,
+		nm:             nm,
+		nmDeleted:      nmDeleted,
+		includeDeleted: fixIncludeDeleted,
 	}
 
 	if err := storage.ScanVolumeFile(basepath, collection, vid, storage.NeedleMapInMemory, scanner); err != nil {
@@ -135,12 +169,12 @@ func doFixOneVolume(basepath string, baseFileName string, collection string, vol
 		}
 	}
 
-	if err := nm.SaveToIdx(indexFileName); err != nil {
+	if err := SaveToIdx(scanner, indexFileName); err != nil {
-		os.Remove(indexFileName)
 		err := fmt.Errorf("save to .idx File: %v", err)
 		if *fixIgnoreError {
 			glog.Error(err)
 		} else {
+			os.Remove(indexFileName)
 			glog.Fatal(err)
 		}
 	}

weed/storage/needle_map_memory.go

@@ -36,8 +36,8 @@ func LoadCompactNeedleMap(file *os.File) (*NeedleMap, error) {
 func doLoading(file *os.File, nm *NeedleMap) (*NeedleMap, error) {
 	e := idx.WalkIndexFile(file, 0, func(key NeedleId, offset Offset, size Size) error {
 		nm.MaybeSetMaxFileKey(key)
-		nm.FileCounter++
 		if !offset.IsZero() && size.IsValid() {
+			nm.FileCounter++
 			nm.FileByteCounter = nm.FileByteCounter + uint64(size)
 			oldOffset, oldSize := nm.m.Set(NeedleId(key), offset, size)
 			if !oldOffset.IsZero() && oldSize.IsValid() {
@@ -51,7 +51,7 @@ func doLoading(file *os.File, nm *NeedleMap) (*NeedleMap, error) {
 		}
 		return nil
 	})
-	glog.V(1).Infof("max file key: %d for file: %s", nm.MaxFileKey(), file.Name())
+	glog.V(1).Infof("max file key: %v count: %d deleted: %d for file: %s", nm.MaxFileKey(), nm.FileCount(), nm.DeletedCount(), file.Name())
 	return nm, e
 }
 

weed/storage/volume_checking.go

@@ -109,9 +109,6 @@ func verifyNeedleIntegrity(datFile backend.BackendStorageFile, v needle.Version,
 			return 0, fmt.Errorf("verifyNeedleIntegrity check %s entry offset %d size %d: %v", datFile.Name(), offset, size, err)
 		}
 		n.AppendAtNs = util.BytesToUint64(bytes)
-		if n.HasTtl() {
-			return n.AppendAtNs, nil
-		}
 		fileTailOffset := offset + needle.GetActualSize(size, v)
 		fileSize, _, err := datFile.GetStat()
 		if err != nil {
@@ -130,7 +127,7 @@ func verifyNeedleIntegrity(datFile backend.BackendStorageFile, v needle.Version,
 		return n.AppendAtNs, fmt.Errorf("read data [%d,%d) : %v", offset, offset+int64(size), err)
 	}
 	if n.Id != key {
-		return n.AppendAtNs, fmt.Errorf("index key %#x does not match needle's Id %#x", key, n.Id)
+		return n.AppendAtNs, fmt.Errorf("index key %v does not match needle's Id %v", key, n.Id)
 	}
 	return n.AppendAtNs, err
 }
@@ -147,7 +144,7 @@ func verifyDeletedNeedleIntegrity(datFile backend.BackendStorageFile, v needle.V
 		return n.AppendAtNs, fmt.Errorf("read data [%d,%d) : %v", fileSize-size, size, err)
 	}
 	if n.Id != key {
-		return n.AppendAtNs, fmt.Errorf("index key %#x does not match needle's Id %#x", key, n.Id)
+		return n.AppendAtNs, fmt.Errorf("index key %v does not match needle's Id %v", key, n.Id)
 	}
 	return n.AppendAtNs, err
 }

weed/storage/volume_vacuum.go

@@ -487,19 +487,21 @@ func (v *Volume) copyDataBasedOnIndexFile(srcDatName, srcIdxName, dstDatName, da
 	if err != nil {
 		return err
 	}
-	dstDatSize, _, err := dstDatBackend.GetStat()
+	if v.Ttl.String() == "" {
-	if err != nil {
+		dstDatSize, _, err := dstDatBackend.GetStat()
-		return err
+		if err != nil {
-	}
+			return err
-	if v.nm.ContentSize() > v.nm.DeletedSize() {
+		}
-		expectedContentSize := v.nm.ContentSize() - v.nm.DeletedSize()
+		if v.nm.ContentSize() > v.nm.DeletedSize() {
-		if expectedContentSize > uint64(dstDatSize) {
+			expectedContentSize := v.nm.ContentSize() - v.nm.DeletedSize()
-			return fmt.Errorf("volume %s unexpected new data size: %d does not match size of content minus deleted: %d",
+			if expectedContentSize > uint64(dstDatSize) {
-				v.Id.String(), dstDatSize, expectedContentSize)
+				return fmt.Errorf("volume %s unexpected new data size: %d does not match size of content minus deleted: %d",
+					v.Id.String(), dstDatSize, expectedContentSize)
+			}
+		} else {
+			glog.Warningf("volume %s content size: %d less deleted size: %d, new size: %d",
+				v.Id.String(), v.nm.ContentSize(), v.nm.DeletedSize(), dstDatSize)
 		}
-	} else {
-		glog.Warningf("volume %s content size: %d less deleted size: %d, new size: %d",
-			v.Id.String(), v.nm.ContentSize(), v.nm.DeletedSize(), dstDatSize)
 	}
 	err = newNm.SaveToIdx(datIdxName)
 	if err != nil {