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)
38 type collectionFileSystem struct {
43 // FileSystem returns a CollectionFileSystem for the collection.
44 func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFileSystem, error) {
46 if c.ModifiedAt == nil {
49 modTime = *c.ModifiedAt
51 fs := &collectionFileSystem{
53 fileSystem: fileSystem{
54 fsBackend: keepBackend{apiClient: client, keepClient: kc},
62 mode: os.ModeDir | 0755,
65 inodes: make(map[string]inode),
68 root.SetParent(root, ".")
69 if err := root.loadManifest(c.ManifestText); err != nil {
72 backdateTree(root, modTime)
77 func backdateTree(n inode, modTime time.Time) {
78 switch n := n.(type) {
80 n.fileinfo.modTime = modTime
82 n.fileinfo.modTime = modTime
83 for _, n := range n.inodes {
84 backdateTree(n, modTime)
89 func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime time.Time) (node inode, err error) {
90 if name == "" || name == "." || name == ".." {
91 return nil, ErrInvalidArgument
99 mode: perm | os.ModeDir,
102 inodes: make(map[string]inode),
110 mode: perm & ^os.ModeDir,
117 func (fs *collectionFileSystem) Sync() error {
118 log.Printf("cfs.Sync()")
122 txt, err := fs.MarshalManifest(".")
124 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
131 err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, fs.UpdateBody(coll), map[string]interface{}{"select": []string{"uuid"}})
133 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
138 func (fs *collectionFileSystem) MarshalManifest(prefix string) (string, error) {
139 fs.fileSystem.root.Lock()
140 defer fs.fileSystem.root.Unlock()
141 return fs.fileSystem.root.(*dirnode).marshalManifest(prefix)
144 func (fs *collectionFileSystem) Size() int64 {
145 return fs.fileSystem.root.(*dirnode).Size()
148 // filenodePtr is an offset into a file that is (usually) efficient to
149 // seek to. Specifically, if filenode.repacked==filenodePtr.repacked
151 // filenode.segments[filenodePtr.segmentIdx][filenodePtr.segmentOff]
152 // corresponds to file offset filenodePtr.off. Otherwise, it is
153 // necessary to reexamine len(filenode.segments[0]) etc. to find the
154 // correct segment and offset.
155 type filenodePtr struct {
162 // seek returns a ptr that is consistent with both startPtr.off and
163 // the current state of fn. The caller must already hold fn.RLock() or
166 // If startPtr is beyond EOF, ptr.segment* will indicate precisely
171 // ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
173 // filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
174 func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
177 // meaningless anyway
179 } else if ptr.off >= fn.fileinfo.size {
180 ptr.segmentIdx = len(fn.segments)
182 ptr.repacked = fn.repacked
184 } else if ptr.repacked == fn.repacked {
185 // segmentIdx and segmentOff accurately reflect
186 // ptr.off, but might have fallen off the end of a
188 if ptr.segmentOff >= fn.segments[ptr.segmentIdx].Len() {
195 ptr.repacked = fn.repacked
197 if ptr.off >= fn.fileinfo.size {
198 ptr.segmentIdx, ptr.segmentOff = len(fn.segments), 0
201 // Recompute segmentIdx and segmentOff. We have already
202 // established fn.fileinfo.size > ptr.off >= 0, so we don't
203 // have to deal with edge cases here.
205 for ptr.segmentIdx, ptr.segmentOff = 0, 0; off < ptr.off; ptr.segmentIdx++ {
206 // This would panic (index out of range) if
207 // fn.fileinfo.size were larger than
208 // sum(fn.segments[i].Len()) -- but that can't happen
209 // because we have ensured fn.fileinfo.size is always
211 segLen := int64(fn.segments[ptr.segmentIdx].Len())
212 if off+segLen > ptr.off {
213 ptr.segmentOff = int(ptr.off - off)
221 // filenode implements inode.
222 type filenode struct {
227 // number of times `segments` has changed in a
228 // way that might invalidate a filenodePtr
230 memsize int64 // bytes in memSegments
235 // caller must have lock
236 func (fn *filenode) appendSegment(e segment) {
237 fn.segments = append(fn.segments, e)
238 fn.fileinfo.size += int64(e.Len())
241 func (fn *filenode) SetParent(p inode, name string) {
245 fn.fileinfo.name = name
248 func (fn *filenode) Parent() inode {
254 func (fn *filenode) FS() FileSystem {
258 // Read reads file data from a single segment, starting at startPtr,
259 // into p. startPtr is assumed not to be up-to-date. Caller must have
261 func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
262 ptr = fn.seek(startPtr)
264 err = ErrNegativeOffset
267 if ptr.segmentIdx >= len(fn.segments) {
271 n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
275 if ptr.segmentOff == fn.segments[ptr.segmentIdx].Len() {
278 if ptr.segmentIdx < len(fn.segments) && err == io.EOF {
286 func (fn *filenode) Size() int64 {
289 return fn.fileinfo.Size()
292 func (fn *filenode) FileInfo() os.FileInfo {
298 func (fn *filenode) Truncate(size int64) error {
301 return fn.truncate(size)
304 func (fn *filenode) truncate(size int64) error {
305 if size == fn.fileinfo.size {
309 if size < fn.fileinfo.size {
310 ptr := fn.seek(filenodePtr{off: size})
311 for i := ptr.segmentIdx; i < len(fn.segments); i++ {
312 if seg, ok := fn.segments[i].(*memSegment); ok {
313 fn.memsize -= int64(seg.Len())
316 if ptr.segmentOff == 0 {
317 fn.segments = fn.segments[:ptr.segmentIdx]
319 fn.segments = fn.segments[:ptr.segmentIdx+1]
320 switch seg := fn.segments[ptr.segmentIdx].(type) {
322 seg.Truncate(ptr.segmentOff)
323 fn.memsize += int64(seg.Len())
325 fn.segments[ptr.segmentIdx] = seg.Slice(0, ptr.segmentOff)
328 fn.fileinfo.size = size
331 for size > fn.fileinfo.size {
332 grow := size - fn.fileinfo.size
335 if len(fn.segments) == 0 {
337 fn.segments = append(fn.segments, seg)
338 } else if seg, ok = fn.segments[len(fn.segments)-1].(*memSegment); !ok || seg.Len() >= maxBlockSize {
340 fn.segments = append(fn.segments, seg)
342 if maxgrow := int64(maxBlockSize - seg.Len()); maxgrow < grow {
345 seg.Truncate(seg.Len() + int(grow))
346 fn.fileinfo.size += grow
352 // Write writes data from p to the file, starting at startPtr,
353 // extending the file size if necessary. Caller must have Lock.
354 func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
355 if startPtr.off > fn.fileinfo.size {
356 if err = fn.truncate(startPtr.off); err != nil {
357 return 0, startPtr, err
360 ptr = fn.seek(startPtr)
362 err = ErrNegativeOffset
365 for len(p) > 0 && err == nil {
367 if len(cando) > maxBlockSize {
368 cando = cando[:maxBlockSize]
370 // Rearrange/grow fn.segments (and shrink cando if
371 // needed) such that cando can be copied to
372 // fn.segments[ptr.segmentIdx] at offset
374 cur := ptr.segmentIdx
375 prev := ptr.segmentIdx - 1
377 if cur < len(fn.segments) {
378 _, curWritable = fn.segments[cur].(*memSegment)
380 var prevAppendable bool
381 if prev >= 0 && fn.segments[prev].Len() < maxBlockSize {
382 _, prevAppendable = fn.segments[prev].(*memSegment)
384 if ptr.segmentOff > 0 && !curWritable {
385 // Split a non-writable block.
386 if max := fn.segments[cur].Len() - ptr.segmentOff; max <= len(cando) {
387 // Truncate cur, and insert a new
390 fn.segments = append(fn.segments, nil)
391 copy(fn.segments[cur+1:], fn.segments[cur:])
393 // Split cur into two copies, truncate
394 // the one on the left, shift the one
395 // on the right, and insert a new
396 // segment between them.
397 fn.segments = append(fn.segments, nil, nil)
398 copy(fn.segments[cur+2:], fn.segments[cur:])
399 fn.segments[cur+2] = fn.segments[cur+2].Slice(ptr.segmentOff+len(cando), -1)
404 seg.Truncate(len(cando))
405 fn.memsize += int64(len(cando))
406 fn.segments[cur] = seg
407 fn.segments[prev] = fn.segments[prev].Slice(0, ptr.segmentOff)
412 } else if curWritable {
413 if fit := int(fn.segments[cur].Len()) - ptr.segmentOff; fit < len(cando) {
418 // Shrink cando if needed to fit in
420 if cangrow := maxBlockSize - fn.segments[prev].Len(); cangrow < len(cando) {
421 cando = cando[:cangrow]
425 if cur == len(fn.segments) {
426 // ptr is at EOF, filesize is changing.
427 fn.fileinfo.size += int64(len(cando))
428 } else if el := fn.segments[cur].Len(); el <= len(cando) {
429 // cando is long enough that we won't
430 // need cur any more. shrink cando to
431 // be exactly as long as cur
432 // (otherwise we'd accidentally shift
433 // the effective position of all
434 // segments after cur).
436 copy(fn.segments[cur:], fn.segments[cur+1:])
437 fn.segments = fn.segments[:len(fn.segments)-1]
439 // shrink cur by the same #bytes we're growing prev
440 fn.segments[cur] = fn.segments[cur].Slice(len(cando), -1)
446 ptr.segmentOff = fn.segments[prev].Len()
447 fn.segments[prev].(*memSegment).Truncate(ptr.segmentOff + len(cando))
448 fn.memsize += int64(len(cando))
452 // Insert a segment between prev and
453 // cur, and advance prev/cur.
454 fn.segments = append(fn.segments, nil)
455 if cur < len(fn.segments) {
456 copy(fn.segments[cur+1:], fn.segments[cur:])
460 // appending a new segment does
461 // not invalidate any ptrs
464 seg.Truncate(len(cando))
465 fn.memsize += int64(len(cando))
466 fn.segments[cur] = seg
472 // Finally we can copy bytes from cando to the current segment.
473 fn.segments[ptr.segmentIdx].(*memSegment).WriteAt(cando, ptr.segmentOff)
477 ptr.off += int64(len(cando))
478 ptr.segmentOff += len(cando)
479 if ptr.segmentOff >= maxBlockSize {
480 fn.pruneMemSegments()
482 if fn.segments[ptr.segmentIdx].Len() == ptr.segmentOff {
487 fn.fileinfo.modTime = time.Now()
492 // Write some data out to disk to reduce memory use. Caller must have
494 func (fn *filenode) pruneMemSegments() {
495 // TODO: async (don't hold Lock() while waiting for Keep)
496 // TODO: share code with (*dirnode)sync()
497 // TODO: pack/flush small blocks too, when fragmented
498 for idx, seg := range fn.segments {
499 seg, ok := seg.(*memSegment)
500 if !ok || seg.Len() < maxBlockSize {
503 locator, _, err := fn.FS().PutB(seg.buf)
505 // TODO: stall (or return errors from)
506 // subsequent writes until flushing
510 fn.memsize -= int64(seg.Len())
511 fn.segments[idx] = storedSegment{
521 type dirnode struct {
522 fs *collectionFileSystem
526 func (dn *dirnode) FS() FileSystem {
530 func (dn *dirnode) Child(name string, replace func(inode) (inode, error)) (inode, error) {
531 if dn == dn.fs.rootnode() && name == ".arvados#collection" {
532 gn := &getternode{Getter: func() ([]byte, error) {
535 coll.ManifestText, err = dn.fs.MarshalManifest(".")
539 data, err := json.Marshal(&coll)
541 data = append(data, '\n')
545 gn.SetParent(dn, name)
548 return dn.treenode.Child(name, replace)
551 // sync flushes in-memory data (for all files in the tree rooted at
552 // dn) to persistent storage. Caller must hold dn.Lock().
553 func (dn *dirnode) sync() error {
554 type shortBlock struct {
558 var pending []shortBlock
561 flush := func(sbs []shortBlock) error {
565 block := make([]byte, 0, maxBlockSize)
566 for _, sb := range sbs {
567 block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...)
569 locator, _, err := dn.fs.PutB(block)
574 for _, sb := range sbs {
575 data := sb.fn.segments[sb.idx].(*memSegment).buf
576 sb.fn.segments[sb.idx] = storedSegment{
584 sb.fn.memsize -= int64(len(data))
589 names := make([]string, 0, len(dn.inodes))
590 for name := range dn.inodes {
591 names = append(names, name)
595 for _, name := range names {
596 fn, ok := dn.inodes[name].(*filenode)
602 for idx, seg := range fn.segments {
603 seg, ok := seg.(*memSegment)
607 if seg.Len() > maxBlockSize/2 {
608 if err := flush([]shortBlock{{fn, idx}}); err != nil {
613 if pendingLen+seg.Len() > maxBlockSize {
614 if err := flush(pending); err != nil {
620 pending = append(pending, shortBlock{fn, idx})
621 pendingLen += seg.Len()
624 return flush(pending)
627 // caller must have read lock.
628 func (dn *dirnode) marshalManifest(prefix string) (string, error) {
630 type filepart struct {
635 var fileparts []filepart
639 if err := dn.sync(); err != nil {
643 names := make([]string, 0, len(dn.inodes))
644 for name, node := range dn.inodes {
645 names = append(names, name)
651 for _, name := range names {
652 switch node := dn.inodes[name].(type) {
654 subdir, err := node.marshalManifest(prefix + "/" + name)
658 subdirs = subdirs + subdir
660 if len(node.segments) == 0 {
661 fileparts = append(fileparts, filepart{name: name})
664 for _, seg := range node.segments {
665 switch seg := seg.(type) {
667 if len(blocks) > 0 && blocks[len(blocks)-1] == seg.locator {
668 streamLen -= int64(seg.size)
670 blocks = append(blocks, seg.locator)
674 offset: streamLen + int64(seg.offset),
675 length: int64(seg.length),
677 if prev := len(fileparts) - 1; prev >= 0 &&
678 fileparts[prev].name == name &&
679 fileparts[prev].offset+fileparts[prev].length == next.offset {
680 fileparts[prev].length += next.length
682 fileparts = append(fileparts, next)
684 streamLen += int64(seg.size)
686 // This can't happen: we
687 // haven't unlocked since
689 panic(fmt.Sprintf("can't marshal segment type %T", seg))
693 panic(fmt.Sprintf("can't marshal inode type %T", node))
696 var filetokens []string
697 for _, s := range fileparts {
698 filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name)))
700 if len(filetokens) == 0 {
702 } else if len(blocks) == 0 {
703 blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"}
705 return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil
708 func (dn *dirnode) loadManifest(txt string) error {
710 streams := strings.Split(txt, "\n")
711 if streams[len(streams)-1] != "" {
712 return fmt.Errorf("line %d: no trailing newline", len(streams))
714 streams = streams[:len(streams)-1]
715 segments := []storedSegment{}
716 for i, stream := range streams {
718 var anyFileTokens bool
721 segments = segments[:0]
722 for i, token := range strings.Split(stream, " ") {
724 dirname = manifestUnescape(token)
727 if !strings.Contains(token, ":") {
729 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
731 toks := strings.SplitN(token, "+", 3)
733 return fmt.Errorf("line %d: bad locator %q", lineno, token)
735 length, err := strconv.ParseInt(toks[1], 10, 32)
736 if err != nil || length < 0 {
737 return fmt.Errorf("line %d: bad locator %q", lineno, token)
739 segments = append(segments, storedSegment{
746 } else if len(segments) == 0 {
747 return fmt.Errorf("line %d: bad locator %q", lineno, token)
750 toks := strings.SplitN(token, ":", 3)
752 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
756 offset, err := strconv.ParseInt(toks[0], 10, 64)
757 if err != nil || offset < 0 {
758 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
760 length, err := strconv.ParseInt(toks[1], 10, 64)
761 if err != nil || length < 0 {
762 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
764 name := dirname + "/" + manifestUnescape(toks[2])
765 fnode, err := dn.createFileAndParents(name)
767 return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err)
769 // Map the stream offset/range coordinates to
770 // block/offset/range coordinates and add
771 // corresponding storedSegments to the filenode
773 // Can't continue where we left off.
774 // TODO: binary search instead of
775 // rewinding all the way (but this
776 // situation might be rare anyway)
779 for next := int64(0); segIdx < len(segments); segIdx++ {
780 seg := segments[segIdx]
781 next = pos + int64(seg.Len())
782 if next <= offset || seg.Len() == 0 {
786 if pos >= offset+length {
791 blkOff = int(offset - pos)
793 blkLen := seg.Len() - blkOff
794 if pos+int64(blkOff+blkLen) > offset+length {
795 blkLen = int(offset + length - pos - int64(blkOff))
797 fnode.appendSegment(storedSegment{
799 locator: seg.locator,
804 if next > offset+length {
810 if segIdx == len(segments) && pos < offset+length {
811 return fmt.Errorf("line %d: invalid segment in %d-byte stream: %q", lineno, pos, token)
815 return fmt.Errorf("line %d: no file segments", lineno)
816 } else if len(segments) == 0 {
817 return fmt.Errorf("line %d: no locators", lineno)
818 } else if dirname == "" {
819 return fmt.Errorf("line %d: no stream name", lineno)
825 // only safe to call from loadManifest -- no locking
826 func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
828 names := strings.Split(path, "/")
829 basename := names[len(names)-1]
830 if !permittedName(basename) {
831 err = fmt.Errorf("invalid file part %q in path %q", basename, path)
834 for _, name := range names[:len(names)-1] {
840 // can't be sure parent will be a *dirnode
841 return nil, ErrInvalidArgument
846 node, err = node.Child(name, func(child inode) (inode, error) {
848 child, err := node.FS().newNode(name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime())
852 child.SetParent(node, name)
854 } else if !child.IsDir() {
855 return child, ErrFileExists
864 _, err = node.Child(basename, func(child inode) (inode, error) {
865 switch child := child.(type) {
867 child, err = node.FS().newNode(basename, 0755, node.FileInfo().ModTime())
871 child.SetParent(node, basename)
872 fn = child.(*filenode)
878 return child, ErrIsDirectory
880 return child, ErrInvalidArgument
886 func (dn *dirnode) Size() (bytes int64) {
889 for _, i := range dn.inodes {
890 switch i := i.(type) {
891 case *filenode, *dirnode:
898 type segment interface {
901 // Return a new segment with a subsection of the data from this
902 // one. length<0 means length=Len()-off.
903 Slice(off int, length int) segment
906 type memSegment struct {
910 func (me *memSegment) Len() int {
914 func (me *memSegment) Slice(off, length int) segment {
916 length = len(me.buf) - off
918 buf := make([]byte, length)
919 copy(buf, me.buf[off:])
920 return &memSegment{buf: buf}
923 func (me *memSegment) Truncate(n int) {
927 newsize = newsize << 2
929 newbuf := make([]byte, n, newsize)
933 // Zero unused part when shrinking, in case we grow
934 // and start using it again later.
935 for i := n; i < len(me.buf); i++ {
942 func (me *memSegment) WriteAt(p []byte, off int) {
943 if off+len(p) > len(me.buf) {
944 panic("overflowed segment")
946 copy(me.buf[off:], p)
949 func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
950 if off > int64(me.Len()) {
954 n = copy(p, me.buf[int(off):])
961 type storedSegment struct {
964 size int // size of stored block (also encoded in locator)
965 offset int // position of segment within the stored block
966 length int // bytes in this segment (offset + length <= size)
969 func (se storedSegment) Len() int {
973 func (se storedSegment) Slice(n, size int) segment {
976 if size >= 0 && se.length > size {
982 func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
983 if off > int64(se.length) {
986 maxlen := se.length - int(off)
989 n, err = se.kc.ReadAt(se.locator, p, int(off)+se.offset)
995 return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
998 func canonicalName(name string) string {
999 name = path.Clean("/" + name)
1000 if name == "/" || name == "./" {
1002 } else if strings.HasPrefix(name, "/") {
1008 var manifestEscapeSeq = regexp.MustCompile(`\\([0-7]{3}|\\)`)
1010 func manifestUnescapeFunc(seq string) string {
1014 i, err := strconv.ParseUint(seq[1:], 8, 8)
1016 // Invalid escape sequence: can't unescape.
1019 return string([]byte{byte(i)})
1022 func manifestUnescape(s string) string {
1023 return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeFunc)
1026 var manifestEscapedChar = regexp.MustCompile(`[\000-\040:\s\\]`)
1028 func manifestEscapeFunc(seq string) string {
1029 return fmt.Sprintf("\\%03o", byte(seq[0]))
1032 func manifestEscape(s string) string {
1033 return manifestEscapedChar.ReplaceAllStringFunc(s, manifestEscapeFunc)