1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: Apache-2.0
22 var maxBlockSize = 1 << 26
24 // A CollectionFileSystem is a FileSystem that can be serialized as a
25 // manifest and stored as a collection.
26 type CollectionFileSystem interface {
29 // Flush all file data to Keep and return a snapshot of the
30 // filesystem suitable for saving as (Collection)ManifestText.
31 // Prefix (normally ".") is a top level directory, effectively
32 // prepended to all paths in the returned manifest.
33 MarshalManifest(prefix string) (string, error)
36 type collectionFileSystem struct {
41 // FileSystem returns a CollectionFileSystem for the collection.
42 func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFileSystem, error) {
44 if c.ModifiedAt == nil {
47 modTime = *c.ModifiedAt
49 fs := &collectionFileSystem{
51 fileSystem: fileSystem{
52 fsBackend: keepBackend{apiClient: client, keepClient: kc},
60 mode: os.ModeDir | 0755,
63 inodes: make(map[string]inode),
67 if err := root.loadManifest(c.ManifestText); err != nil {
74 func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime time.Time) (node inode, err error) {
75 if name == "" || name == "." || name == ".." {
76 return nil, ErrInvalidArgument
84 mode: perm | os.ModeDir,
87 inodes: make(map[string]inode),
95 mode: perm & ^os.ModeDir,
102 func (fs *collectionFileSystem) Sync() error {
103 log.Printf("cfs.Sync()")
107 txt, err := fs.MarshalManifest(".")
109 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
116 err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, fs.UpdateBody(coll), map[string]interface{}{"select": []string{"uuid"}})
118 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
123 func (fs *collectionFileSystem) MarshalManifest(prefix string) (string, error) {
124 fs.fileSystem.root.Lock()
125 defer fs.fileSystem.root.Unlock()
126 return fs.fileSystem.root.(*dirnode).marshalManifest(prefix)
129 // filenodePtr is an offset into a file that is (usually) efficient to
130 // seek to. Specifically, if filenode.repacked==filenodePtr.repacked
132 // filenode.segments[filenodePtr.segmentIdx][filenodePtr.segmentOff]
133 // corresponds to file offset filenodePtr.off. Otherwise, it is
134 // necessary to reexamine len(filenode.segments[0]) etc. to find the
135 // correct segment and offset.
136 type filenodePtr struct {
143 // seek returns a ptr that is consistent with both startPtr.off and
144 // the current state of fn. The caller must already hold fn.RLock() or
147 // If startPtr is beyond EOF, ptr.segment* will indicate precisely
152 // ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
154 // filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
155 func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
158 // meaningless anyway
160 } else if ptr.off >= fn.fileinfo.size {
161 ptr.segmentIdx = len(fn.segments)
163 ptr.repacked = fn.repacked
165 } else if ptr.repacked == fn.repacked {
166 // segmentIdx and segmentOff accurately reflect
167 // ptr.off, but might have fallen off the end of a
169 if ptr.segmentOff >= fn.segments[ptr.segmentIdx].Len() {
176 ptr.repacked = fn.repacked
178 if ptr.off >= fn.fileinfo.size {
179 ptr.segmentIdx, ptr.segmentOff = len(fn.segments), 0
182 // Recompute segmentIdx and segmentOff. We have already
183 // established fn.fileinfo.size > ptr.off >= 0, so we don't
184 // have to deal with edge cases here.
186 for ptr.segmentIdx, ptr.segmentOff = 0, 0; off < ptr.off; ptr.segmentIdx++ {
187 // This would panic (index out of range) if
188 // fn.fileinfo.size were larger than
189 // sum(fn.segments[i].Len()) -- but that can't happen
190 // because we have ensured fn.fileinfo.size is always
192 segLen := int64(fn.segments[ptr.segmentIdx].Len())
193 if off+segLen > ptr.off {
194 ptr.segmentOff = int(ptr.off - off)
202 // filenode implements inode.
203 type filenode struct {
208 // number of times `segments` has changed in a
209 // way that might invalidate a filenodePtr
211 memsize int64 // bytes in memSegments
216 // caller must have lock
217 func (fn *filenode) appendSegment(e segment) {
218 fn.segments = append(fn.segments, e)
219 fn.fileinfo.size += int64(e.Len())
222 func (fn *filenode) SetParent(p inode) {
228 func (fn *filenode) Parent() inode {
234 func (fn *filenode) FS() FileSystem {
238 // Read reads file data from a single segment, starting at startPtr,
239 // into p. startPtr is assumed not to be up-to-date. Caller must have
241 func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
242 ptr = fn.seek(startPtr)
244 err = ErrNegativeOffset
247 if ptr.segmentIdx >= len(fn.segments) {
251 n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
255 if ptr.segmentOff == fn.segments[ptr.segmentIdx].Len() {
258 if ptr.segmentIdx < len(fn.segments) && err == io.EOF {
266 func (fn *filenode) Size() int64 {
269 return fn.fileinfo.Size()
272 func (fn *filenode) FileInfo() os.FileInfo {
278 func (fn *filenode) Truncate(size int64) error {
281 return fn.truncate(size)
284 func (fn *filenode) truncate(size int64) error {
285 if size == fn.fileinfo.size {
289 if size < fn.fileinfo.size {
290 ptr := fn.seek(filenodePtr{off: size})
291 for i := ptr.segmentIdx; i < len(fn.segments); i++ {
292 if seg, ok := fn.segments[i].(*memSegment); ok {
293 fn.memsize -= int64(seg.Len())
296 if ptr.segmentOff == 0 {
297 fn.segments = fn.segments[:ptr.segmentIdx]
299 fn.segments = fn.segments[:ptr.segmentIdx+1]
300 switch seg := fn.segments[ptr.segmentIdx].(type) {
302 seg.Truncate(ptr.segmentOff)
303 fn.memsize += int64(seg.Len())
305 fn.segments[ptr.segmentIdx] = seg.Slice(0, ptr.segmentOff)
308 fn.fileinfo.size = size
311 for size > fn.fileinfo.size {
312 grow := size - fn.fileinfo.size
315 if len(fn.segments) == 0 {
317 fn.segments = append(fn.segments, seg)
318 } else if seg, ok = fn.segments[len(fn.segments)-1].(*memSegment); !ok || seg.Len() >= maxBlockSize {
320 fn.segments = append(fn.segments, seg)
322 if maxgrow := int64(maxBlockSize - seg.Len()); maxgrow < grow {
325 seg.Truncate(seg.Len() + int(grow))
326 fn.fileinfo.size += grow
332 // Write writes data from p to the file, starting at startPtr,
333 // extending the file size if necessary. Caller must have Lock.
334 func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
335 if startPtr.off > fn.fileinfo.size {
336 if err = fn.truncate(startPtr.off); err != nil {
337 return 0, startPtr, err
340 ptr = fn.seek(startPtr)
342 err = ErrNegativeOffset
345 for len(p) > 0 && err == nil {
347 if len(cando) > maxBlockSize {
348 cando = cando[:maxBlockSize]
350 // Rearrange/grow fn.segments (and shrink cando if
351 // needed) such that cando can be copied to
352 // fn.segments[ptr.segmentIdx] at offset
354 cur := ptr.segmentIdx
355 prev := ptr.segmentIdx - 1
357 if cur < len(fn.segments) {
358 _, curWritable = fn.segments[cur].(*memSegment)
360 var prevAppendable bool
361 if prev >= 0 && fn.segments[prev].Len() < maxBlockSize {
362 _, prevAppendable = fn.segments[prev].(*memSegment)
364 if ptr.segmentOff > 0 && !curWritable {
365 // Split a non-writable block.
366 if max := fn.segments[cur].Len() - ptr.segmentOff; max <= len(cando) {
367 // Truncate cur, and insert a new
370 fn.segments = append(fn.segments, nil)
371 copy(fn.segments[cur+1:], fn.segments[cur:])
373 // Split cur into two copies, truncate
374 // the one on the left, shift the one
375 // on the right, and insert a new
376 // segment between them.
377 fn.segments = append(fn.segments, nil, nil)
378 copy(fn.segments[cur+2:], fn.segments[cur:])
379 fn.segments[cur+2] = fn.segments[cur+2].Slice(ptr.segmentOff+len(cando), -1)
384 seg.Truncate(len(cando))
385 fn.memsize += int64(len(cando))
386 fn.segments[cur] = seg
387 fn.segments[prev] = fn.segments[prev].Slice(0, ptr.segmentOff)
392 } else if curWritable {
393 if fit := int(fn.segments[cur].Len()) - ptr.segmentOff; fit < len(cando) {
398 // Shrink cando if needed to fit in
400 if cangrow := maxBlockSize - fn.segments[prev].Len(); cangrow < len(cando) {
401 cando = cando[:cangrow]
405 if cur == len(fn.segments) {
406 // ptr is at EOF, filesize is changing.
407 fn.fileinfo.size += int64(len(cando))
408 } else if el := fn.segments[cur].Len(); el <= len(cando) {
409 // cando is long enough that we won't
410 // need cur any more. shrink cando to
411 // be exactly as long as cur
412 // (otherwise we'd accidentally shift
413 // the effective position of all
414 // segments after cur).
416 copy(fn.segments[cur:], fn.segments[cur+1:])
417 fn.segments = fn.segments[:len(fn.segments)-1]
419 // shrink cur by the same #bytes we're growing prev
420 fn.segments[cur] = fn.segments[cur].Slice(len(cando), -1)
426 ptr.segmentOff = fn.segments[prev].Len()
427 fn.segments[prev].(*memSegment).Truncate(ptr.segmentOff + len(cando))
428 fn.memsize += int64(len(cando))
432 // Insert a segment between prev and
433 // cur, and advance prev/cur.
434 fn.segments = append(fn.segments, nil)
435 if cur < len(fn.segments) {
436 copy(fn.segments[cur+1:], fn.segments[cur:])
440 // appending a new segment does
441 // not invalidate any ptrs
444 seg.Truncate(len(cando))
445 fn.memsize += int64(len(cando))
446 fn.segments[cur] = seg
452 // Finally we can copy bytes from cando to the current segment.
453 fn.segments[ptr.segmentIdx].(*memSegment).WriteAt(cando, ptr.segmentOff)
457 ptr.off += int64(len(cando))
458 ptr.segmentOff += len(cando)
459 if ptr.segmentOff >= maxBlockSize {
460 fn.pruneMemSegments()
462 if fn.segments[ptr.segmentIdx].Len() == ptr.segmentOff {
467 fn.fileinfo.modTime = time.Now()
472 // Write some data out to disk to reduce memory use. Caller must have
474 func (fn *filenode) pruneMemSegments() {
475 // TODO: async (don't hold Lock() while waiting for Keep)
476 // TODO: share code with (*dirnode)sync()
477 // TODO: pack/flush small blocks too, when fragmented
478 for idx, seg := range fn.segments {
479 seg, ok := seg.(*memSegment)
480 if !ok || seg.Len() < maxBlockSize {
483 locator, _, err := fn.FS().PutB(seg.buf)
485 // TODO: stall (or return errors from)
486 // subsequent writes until flushing
490 fn.memsize -= int64(seg.Len())
491 fn.segments[idx] = storedSegment{
501 type dirnode struct {
502 fs *collectionFileSystem
506 func (dn *dirnode) FS() FileSystem {
510 func (dn *dirnode) Child(name string, replace func(inode) inode) inode {
511 if dn == dn.fs.rootnode() && name == ".arvados#collection" {
512 gn := &getternode{Getter: func() ([]byte, error) {
515 coll.ManifestText, err = dn.fs.MarshalManifest(".")
519 data, err := json.Marshal(&coll)
521 data = append(data, 10)
528 return dn.treenode.Child(name, replace)
531 // sync flushes in-memory data (for all files in the tree rooted at
532 // dn) to persistent storage. Caller must hold dn.Lock().
533 func (dn *dirnode) sync() error {
534 type shortBlock struct {
538 var pending []shortBlock
541 flush := func(sbs []shortBlock) error {
545 block := make([]byte, 0, maxBlockSize)
546 for _, sb := range sbs {
547 block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...)
549 locator, _, err := dn.fs.PutB(block)
554 for _, sb := range sbs {
555 data := sb.fn.segments[sb.idx].(*memSegment).buf
556 sb.fn.segments[sb.idx] = storedSegment{
564 sb.fn.memsize -= int64(len(data))
569 names := make([]string, 0, len(dn.inodes))
570 for name := range dn.inodes {
571 names = append(names, name)
575 for _, name := range names {
576 fn, ok := dn.inodes[name].(*filenode)
582 for idx, seg := range fn.segments {
583 seg, ok := seg.(*memSegment)
587 if seg.Len() > maxBlockSize/2 {
588 if err := flush([]shortBlock{{fn, idx}}); err != nil {
593 if pendingLen+seg.Len() > maxBlockSize {
594 if err := flush(pending); err != nil {
600 pending = append(pending, shortBlock{fn, idx})
601 pendingLen += seg.Len()
604 return flush(pending)
607 // caller must have read lock.
608 func (dn *dirnode) marshalManifest(prefix string) (string, error) {
610 type filepart struct {
615 var fileparts []filepart
619 if err := dn.sync(); err != nil {
623 names := make([]string, 0, len(dn.inodes))
624 for name, node := range dn.inodes {
625 names = append(names, name)
631 for _, name := range names {
632 switch node := dn.inodes[name].(type) {
634 subdir, err := node.marshalManifest(prefix + "/" + name)
638 subdirs = subdirs + subdir
640 if len(node.segments) == 0 {
641 fileparts = append(fileparts, filepart{name: name})
644 for _, seg := range node.segments {
645 switch seg := seg.(type) {
647 if len(blocks) > 0 && blocks[len(blocks)-1] == seg.locator {
648 streamLen -= int64(seg.size)
650 blocks = append(blocks, seg.locator)
654 offset: streamLen + int64(seg.offset),
655 length: int64(seg.length),
657 if prev := len(fileparts) - 1; prev >= 0 &&
658 fileparts[prev].name == name &&
659 fileparts[prev].offset+fileparts[prev].length == next.offset {
660 fileparts[prev].length += next.length
662 fileparts = append(fileparts, next)
664 streamLen += int64(seg.size)
666 // This can't happen: we
667 // haven't unlocked since
669 panic(fmt.Sprintf("can't marshal segment type %T", seg))
673 panic(fmt.Sprintf("can't marshal inode type %T", node))
676 var filetokens []string
677 for _, s := range fileparts {
678 filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name)))
680 if len(filetokens) == 0 {
682 } else if len(blocks) == 0 {
683 blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"}
685 return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil
688 func (dn *dirnode) loadManifest(txt string) error {
690 streams := strings.Split(txt, "\n")
691 if streams[len(streams)-1] != "" {
692 return fmt.Errorf("line %d: no trailing newline", len(streams))
694 streams = streams[:len(streams)-1]
695 segments := []storedSegment{}
696 for i, stream := range streams {
698 var anyFileTokens bool
701 segments = segments[:0]
702 for i, token := range strings.Split(stream, " ") {
704 dirname = manifestUnescape(token)
707 if !strings.Contains(token, ":") {
709 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
711 toks := strings.SplitN(token, "+", 3)
713 return fmt.Errorf("line %d: bad locator %q", lineno, token)
715 length, err := strconv.ParseInt(toks[1], 10, 32)
716 if err != nil || length < 0 {
717 return fmt.Errorf("line %d: bad locator %q", lineno, token)
719 segments = append(segments, storedSegment{
726 } else if len(segments) == 0 {
727 return fmt.Errorf("line %d: bad locator %q", lineno, token)
730 toks := strings.SplitN(token, ":", 3)
732 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
736 offset, err := strconv.ParseInt(toks[0], 10, 64)
737 if err != nil || offset < 0 {
738 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
740 length, err := strconv.ParseInt(toks[1], 10, 64)
741 if err != nil || length < 0 {
742 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
744 name := dirname + "/" + manifestUnescape(toks[2])
745 fnode, err := dn.createFileAndParents(name)
747 return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err)
749 // Map the stream offset/range coordinates to
750 // block/offset/range coordinates and add
751 // corresponding storedSegments to the filenode
753 // Can't continue where we left off.
754 // TODO: binary search instead of
755 // rewinding all the way (but this
756 // situation might be rare anyway)
759 for next := int64(0); segIdx < len(segments); segIdx++ {
760 seg := segments[segIdx]
761 next = pos + int64(seg.Len())
762 if next <= offset || seg.Len() == 0 {
766 if pos >= offset+length {
771 blkOff = int(offset - pos)
773 blkLen := seg.Len() - blkOff
774 if pos+int64(blkOff+blkLen) > offset+length {
775 blkLen = int(offset + length - pos - int64(blkOff))
777 fnode.appendSegment(storedSegment{
779 locator: seg.locator,
784 if next > offset+length {
790 if segIdx == len(segments) && pos < offset+length {
791 return fmt.Errorf("line %d: invalid segment in %d-byte stream: %q", lineno, pos, token)
795 return fmt.Errorf("line %d: no file segments", lineno)
796 } else if len(segments) == 0 {
797 return fmt.Errorf("line %d: no locators", lineno)
798 } else if dirname == "" {
799 return fmt.Errorf("line %d: no stream name", lineno)
805 // only safe to call from loadManifest -- no locking
806 func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
808 names := strings.Split(path, "/")
809 basename := names[len(names)-1]
810 if basename == "" || basename == "." || basename == ".." {
811 err = fmt.Errorf("invalid filename")
814 for _, name := range names[:len(names)-1] {
820 // can't be sure parent will be a *dirnode
821 return nil, ErrInvalidArgument
826 node.Child(name, func(child inode) inode {
828 node, err = node.FS().newNode(name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime())
830 } else if !child.IsDir() {
841 node.Child(basename, func(child inode) inode {
842 switch child := child.(type) {
844 child, err = node.FS().newNode(basename, 0755, node.FileInfo().ModTime())
845 fn = child.(*filenode)
854 err = ErrInvalidArgument
861 type segment interface {
864 // Return a new segment with a subsection of the data from this
865 // one. length<0 means length=Len()-off.
866 Slice(off int, length int) segment
869 type memSegment struct {
873 func (me *memSegment) Len() int {
877 func (me *memSegment) Slice(off, length int) segment {
879 length = len(me.buf) - off
881 buf := make([]byte, length)
882 copy(buf, me.buf[off:])
883 return &memSegment{buf: buf}
886 func (me *memSegment) Truncate(n int) {
890 newsize = newsize << 2
892 newbuf := make([]byte, n, newsize)
896 // Zero unused part when shrinking, in case we grow
897 // and start using it again later.
898 for i := n; i < len(me.buf); i++ {
905 func (me *memSegment) WriteAt(p []byte, off int) {
906 if off+len(p) > len(me.buf) {
907 panic("overflowed segment")
909 copy(me.buf[off:], p)
912 func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
913 if off > int64(me.Len()) {
917 n = copy(p, me.buf[int(off):])
924 type storedSegment struct {
927 size int // size of stored block (also encoded in locator)
928 offset int // position of segment within the stored block
929 length int // bytes in this segment (offset + length <= size)
932 func (se storedSegment) Len() int {
936 func (se storedSegment) Slice(n, size int) segment {
939 if size >= 0 && se.length > size {
945 func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
946 if off > int64(se.length) {
949 maxlen := se.length - int(off)
952 n, err = se.kc.ReadAt(se.locator, p, int(off)+se.offset)
958 return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
961 func canonicalName(name string) string {
962 name = path.Clean("/" + name)
963 if name == "/" || name == "./" {
965 } else if strings.HasPrefix(name, "/") {
971 var manifestEscapeSeq = regexp.MustCompile(`\\([0-7]{3}|\\)`)
973 func manifestUnescapeFunc(seq string) string {
977 i, err := strconv.ParseUint(seq[1:], 8, 8)
979 // Invalid escape sequence: can't unescape.
982 return string([]byte{byte(i)})
985 func manifestUnescape(s string) string {
986 return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeFunc)
989 var manifestEscapedChar = regexp.MustCompile(`[\000-\040:\s\\]`)
991 func manifestEscapeFunc(seq string) string {
992 return fmt.Sprintf("\\%03o", byte(seq[0]))
995 func manifestEscape(s string) string {
996 return manifestEscapedChar.ReplaceAllStringFunc(s, manifestEscapeFunc)