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),
66 root.SetParent(root, ".")
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, name string) {
226 fn.fileinfo.name = name
229 func (fn *filenode) Parent() inode {
235 func (fn *filenode) FS() FileSystem {
239 // Read reads file data from a single segment, starting at startPtr,
240 // into p. startPtr is assumed not to be up-to-date. Caller must have
242 func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
243 ptr = fn.seek(startPtr)
245 err = ErrNegativeOffset
248 if ptr.segmentIdx >= len(fn.segments) {
252 n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
256 if ptr.segmentOff == fn.segments[ptr.segmentIdx].Len() {
259 if ptr.segmentIdx < len(fn.segments) && err == io.EOF {
267 func (fn *filenode) Size() int64 {
270 return fn.fileinfo.Size()
273 func (fn *filenode) FileInfo() os.FileInfo {
279 func (fn *filenode) Truncate(size int64) error {
282 return fn.truncate(size)
285 func (fn *filenode) truncate(size int64) error {
286 if size == fn.fileinfo.size {
290 if size < fn.fileinfo.size {
291 ptr := fn.seek(filenodePtr{off: size})
292 for i := ptr.segmentIdx; i < len(fn.segments); i++ {
293 if seg, ok := fn.segments[i].(*memSegment); ok {
294 fn.memsize -= int64(seg.Len())
297 if ptr.segmentOff == 0 {
298 fn.segments = fn.segments[:ptr.segmentIdx]
300 fn.segments = fn.segments[:ptr.segmentIdx+1]
301 switch seg := fn.segments[ptr.segmentIdx].(type) {
303 seg.Truncate(ptr.segmentOff)
304 fn.memsize += int64(seg.Len())
306 fn.segments[ptr.segmentIdx] = seg.Slice(0, ptr.segmentOff)
309 fn.fileinfo.size = size
312 for size > fn.fileinfo.size {
313 grow := size - fn.fileinfo.size
316 if len(fn.segments) == 0 {
318 fn.segments = append(fn.segments, seg)
319 } else if seg, ok = fn.segments[len(fn.segments)-1].(*memSegment); !ok || seg.Len() >= maxBlockSize {
321 fn.segments = append(fn.segments, seg)
323 if maxgrow := int64(maxBlockSize - seg.Len()); maxgrow < grow {
326 seg.Truncate(seg.Len() + int(grow))
327 fn.fileinfo.size += grow
333 // Write writes data from p to the file, starting at startPtr,
334 // extending the file size if necessary. Caller must have Lock.
335 func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
336 if startPtr.off > fn.fileinfo.size {
337 if err = fn.truncate(startPtr.off); err != nil {
338 return 0, startPtr, err
341 ptr = fn.seek(startPtr)
343 err = ErrNegativeOffset
346 for len(p) > 0 && err == nil {
348 if len(cando) > maxBlockSize {
349 cando = cando[:maxBlockSize]
351 // Rearrange/grow fn.segments (and shrink cando if
352 // needed) such that cando can be copied to
353 // fn.segments[ptr.segmentIdx] at offset
355 cur := ptr.segmentIdx
356 prev := ptr.segmentIdx - 1
358 if cur < len(fn.segments) {
359 _, curWritable = fn.segments[cur].(*memSegment)
361 var prevAppendable bool
362 if prev >= 0 && fn.segments[prev].Len() < maxBlockSize {
363 _, prevAppendable = fn.segments[prev].(*memSegment)
365 if ptr.segmentOff > 0 && !curWritable {
366 // Split a non-writable block.
367 if max := fn.segments[cur].Len() - ptr.segmentOff; max <= len(cando) {
368 // Truncate cur, and insert a new
371 fn.segments = append(fn.segments, nil)
372 copy(fn.segments[cur+1:], fn.segments[cur:])
374 // Split cur into two copies, truncate
375 // the one on the left, shift the one
376 // on the right, and insert a new
377 // segment between them.
378 fn.segments = append(fn.segments, nil, nil)
379 copy(fn.segments[cur+2:], fn.segments[cur:])
380 fn.segments[cur+2] = fn.segments[cur+2].Slice(ptr.segmentOff+len(cando), -1)
385 seg.Truncate(len(cando))
386 fn.memsize += int64(len(cando))
387 fn.segments[cur] = seg
388 fn.segments[prev] = fn.segments[prev].Slice(0, ptr.segmentOff)
393 } else if curWritable {
394 if fit := int(fn.segments[cur].Len()) - ptr.segmentOff; fit < len(cando) {
399 // Shrink cando if needed to fit in
401 if cangrow := maxBlockSize - fn.segments[prev].Len(); cangrow < len(cando) {
402 cando = cando[:cangrow]
406 if cur == len(fn.segments) {
407 // ptr is at EOF, filesize is changing.
408 fn.fileinfo.size += int64(len(cando))
409 } else if el := fn.segments[cur].Len(); el <= len(cando) {
410 // cando is long enough that we won't
411 // need cur any more. shrink cando to
412 // be exactly as long as cur
413 // (otherwise we'd accidentally shift
414 // the effective position of all
415 // segments after cur).
417 copy(fn.segments[cur:], fn.segments[cur+1:])
418 fn.segments = fn.segments[:len(fn.segments)-1]
420 // shrink cur by the same #bytes we're growing prev
421 fn.segments[cur] = fn.segments[cur].Slice(len(cando), -1)
427 ptr.segmentOff = fn.segments[prev].Len()
428 fn.segments[prev].(*memSegment).Truncate(ptr.segmentOff + len(cando))
429 fn.memsize += int64(len(cando))
433 // Insert a segment between prev and
434 // cur, and advance prev/cur.
435 fn.segments = append(fn.segments, nil)
436 if cur < len(fn.segments) {
437 copy(fn.segments[cur+1:], fn.segments[cur:])
441 // appending a new segment does
442 // not invalidate any ptrs
445 seg.Truncate(len(cando))
446 fn.memsize += int64(len(cando))
447 fn.segments[cur] = seg
453 // Finally we can copy bytes from cando to the current segment.
454 fn.segments[ptr.segmentIdx].(*memSegment).WriteAt(cando, ptr.segmentOff)
458 ptr.off += int64(len(cando))
459 ptr.segmentOff += len(cando)
460 if ptr.segmentOff >= maxBlockSize {
461 fn.pruneMemSegments()
463 if fn.segments[ptr.segmentIdx].Len() == ptr.segmentOff {
468 fn.fileinfo.modTime = time.Now()
473 // Write some data out to disk to reduce memory use. Caller must have
475 func (fn *filenode) pruneMemSegments() {
476 // TODO: async (don't hold Lock() while waiting for Keep)
477 // TODO: share code with (*dirnode)sync()
478 // TODO: pack/flush small blocks too, when fragmented
479 for idx, seg := range fn.segments {
480 seg, ok := seg.(*memSegment)
481 if !ok || seg.Len() < maxBlockSize {
484 locator, _, err := fn.FS().PutB(seg.buf)
486 // TODO: stall (or return errors from)
487 // subsequent writes until flushing
491 fn.memsize -= int64(seg.Len())
492 fn.segments[idx] = storedSegment{
502 type dirnode struct {
503 fs *collectionFileSystem
507 func (dn *dirnode) FS() FileSystem {
511 func (dn *dirnode) Child(name string, replace func(inode) inode) inode {
512 if dn == dn.fs.rootnode() && name == ".arvados#collection" {
513 gn := &getternode{Getter: func() ([]byte, error) {
516 coll.ManifestText, err = dn.fs.MarshalManifest(".")
520 data, err := json.Marshal(&coll)
522 data = append(data, 10)
526 gn.SetParent(dn, name)
529 return dn.treenode.Child(name, replace)
532 // sync flushes in-memory data (for all files in the tree rooted at
533 // dn) to persistent storage. Caller must hold dn.Lock().
534 func (dn *dirnode) sync() error {
535 type shortBlock struct {
539 var pending []shortBlock
542 flush := func(sbs []shortBlock) error {
546 block := make([]byte, 0, maxBlockSize)
547 for _, sb := range sbs {
548 block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...)
550 locator, _, err := dn.fs.PutB(block)
555 for _, sb := range sbs {
556 data := sb.fn.segments[sb.idx].(*memSegment).buf
557 sb.fn.segments[sb.idx] = storedSegment{
565 sb.fn.memsize -= int64(len(data))
570 names := make([]string, 0, len(dn.inodes))
571 for name := range dn.inodes {
572 names = append(names, name)
576 for _, name := range names {
577 fn, ok := dn.inodes[name].(*filenode)
583 for idx, seg := range fn.segments {
584 seg, ok := seg.(*memSegment)
588 if seg.Len() > maxBlockSize/2 {
589 if err := flush([]shortBlock{{fn, idx}}); err != nil {
594 if pendingLen+seg.Len() > maxBlockSize {
595 if err := flush(pending); err != nil {
601 pending = append(pending, shortBlock{fn, idx})
602 pendingLen += seg.Len()
605 return flush(pending)
608 // caller must have read lock.
609 func (dn *dirnode) marshalManifest(prefix string) (string, error) {
611 type filepart struct {
616 var fileparts []filepart
620 if err := dn.sync(); err != nil {
624 names := make([]string, 0, len(dn.inodes))
625 for name, node := range dn.inodes {
626 names = append(names, name)
632 for _, name := range names {
633 switch node := dn.inodes[name].(type) {
635 subdir, err := node.marshalManifest(prefix + "/" + name)
639 subdirs = subdirs + subdir
641 if len(node.segments) == 0 {
642 fileparts = append(fileparts, filepart{name: name})
645 for _, seg := range node.segments {
646 switch seg := seg.(type) {
648 if len(blocks) > 0 && blocks[len(blocks)-1] == seg.locator {
649 streamLen -= int64(seg.size)
651 blocks = append(blocks, seg.locator)
655 offset: streamLen + int64(seg.offset),
656 length: int64(seg.length),
658 if prev := len(fileparts) - 1; prev >= 0 &&
659 fileparts[prev].name == name &&
660 fileparts[prev].offset+fileparts[prev].length == next.offset {
661 fileparts[prev].length += next.length
663 fileparts = append(fileparts, next)
665 streamLen += int64(seg.size)
667 // This can't happen: we
668 // haven't unlocked since
670 panic(fmt.Sprintf("can't marshal segment type %T", seg))
674 panic(fmt.Sprintf("can't marshal inode type %T", node))
677 var filetokens []string
678 for _, s := range fileparts {
679 filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name)))
681 if len(filetokens) == 0 {
683 } else if len(blocks) == 0 {
684 blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"}
686 return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil
689 func (dn *dirnode) loadManifest(txt string) error {
691 streams := strings.Split(txt, "\n")
692 if streams[len(streams)-1] != "" {
693 return fmt.Errorf("line %d: no trailing newline", len(streams))
695 streams = streams[:len(streams)-1]
696 segments := []storedSegment{}
697 for i, stream := range streams {
699 var anyFileTokens bool
702 segments = segments[:0]
703 for i, token := range strings.Split(stream, " ") {
705 dirname = manifestUnescape(token)
708 if !strings.Contains(token, ":") {
710 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
712 toks := strings.SplitN(token, "+", 3)
714 return fmt.Errorf("line %d: bad locator %q", lineno, token)
716 length, err := strconv.ParseInt(toks[1], 10, 32)
717 if err != nil || length < 0 {
718 return fmt.Errorf("line %d: bad locator %q", lineno, token)
720 segments = append(segments, storedSegment{
727 } else if len(segments) == 0 {
728 return fmt.Errorf("line %d: bad locator %q", lineno, token)
731 toks := strings.SplitN(token, ":", 3)
733 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
737 offset, err := strconv.ParseInt(toks[0], 10, 64)
738 if err != nil || offset < 0 {
739 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
741 length, err := strconv.ParseInt(toks[1], 10, 64)
742 if err != nil || length < 0 {
743 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
745 name := dirname + "/" + manifestUnescape(toks[2])
746 fnode, err := dn.createFileAndParents(name)
748 return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err)
750 // Map the stream offset/range coordinates to
751 // block/offset/range coordinates and add
752 // corresponding storedSegments to the filenode
754 // Can't continue where we left off.
755 // TODO: binary search instead of
756 // rewinding all the way (but this
757 // situation might be rare anyway)
760 for next := int64(0); segIdx < len(segments); segIdx++ {
761 seg := segments[segIdx]
762 next = pos + int64(seg.Len())
763 if next <= offset || seg.Len() == 0 {
767 if pos >= offset+length {
772 blkOff = int(offset - pos)
774 blkLen := seg.Len() - blkOff
775 if pos+int64(blkOff+blkLen) > offset+length {
776 blkLen = int(offset + length - pos - int64(blkOff))
778 fnode.appendSegment(storedSegment{
780 locator: seg.locator,
785 if next > offset+length {
791 if segIdx == len(segments) && pos < offset+length {
792 return fmt.Errorf("line %d: invalid segment in %d-byte stream: %q", lineno, pos, token)
796 return fmt.Errorf("line %d: no file segments", lineno)
797 } else if len(segments) == 0 {
798 return fmt.Errorf("line %d: no locators", lineno)
799 } else if dirname == "" {
800 return fmt.Errorf("line %d: no stream name", lineno)
806 // only safe to call from loadManifest -- no locking
807 func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
809 names := strings.Split(path, "/")
810 basename := names[len(names)-1]
811 if basename == "" || basename == "." || basename == ".." {
812 err = fmt.Errorf("invalid filename")
815 for _, name := range names[:len(names)-1] {
821 // can't be sure parent will be a *dirnode
822 return nil, ErrInvalidArgument
827 node.Child(name, func(child inode) inode {
829 node, err = node.FS().newNode(name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime())
831 } else if !child.IsDir() {
842 node.Child(basename, func(child inode) inode {
843 switch child := child.(type) {
845 child, err = node.FS().newNode(basename, 0755, node.FileInfo().ModTime())
846 fn = child.(*filenode)
855 err = ErrInvalidArgument
862 type segment interface {
865 // Return a new segment with a subsection of the data from this
866 // one. length<0 means length=Len()-off.
867 Slice(off int, length int) segment
870 type memSegment struct {
874 func (me *memSegment) Len() int {
878 func (me *memSegment) Slice(off, length int) segment {
880 length = len(me.buf) - off
882 buf := make([]byte, length)
883 copy(buf, me.buf[off:])
884 return &memSegment{buf: buf}
887 func (me *memSegment) Truncate(n int) {
891 newsize = newsize << 2
893 newbuf := make([]byte, n, newsize)
897 // Zero unused part when shrinking, in case we grow
898 // and start using it again later.
899 for i := n; i < len(me.buf); i++ {
906 func (me *memSegment) WriteAt(p []byte, off int) {
907 if off+len(p) > len(me.buf) {
908 panic("overflowed segment")
910 copy(me.buf[off:], p)
913 func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
914 if off > int64(me.Len()) {
918 n = copy(p, me.buf[int(off):])
925 type storedSegment struct {
928 size int // size of stored block (also encoded in locator)
929 offset int // position of segment within the stored block
930 length int // bytes in this segment (offset + length <= size)
933 func (se storedSegment) Len() int {
937 func (se storedSegment) Slice(n, size int) segment {
940 if size >= 0 && se.length > size {
946 func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
947 if off > int64(se.length) {
950 maxlen := se.length - int(off)
953 n, err = se.kc.ReadAt(se.locator, p, int(off)+se.offset)
959 return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
962 func canonicalName(name string) string {
963 name = path.Clean("/" + name)
964 if name == "/" || name == "./" {
966 } else if strings.HasPrefix(name, "/") {
972 var manifestEscapeSeq = regexp.MustCompile(`\\([0-7]{3}|\\)`)
974 func manifestUnescapeFunc(seq string) string {
978 i, err := strconv.ParseUint(seq[1:], 8, 8)
980 // Invalid escape sequence: can't unescape.
983 return string([]byte{byte(i)})
986 func manifestUnescape(s string) string {
987 return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeFunc)
990 var manifestEscapedChar = regexp.MustCompile(`[\000-\040:\s\\]`)
992 func manifestEscapeFunc(seq string) string {
993 return fmt.Sprintf("\\%03o", byte(seq[0]))
996 func manifestEscape(s string) string {
997 return manifestEscapedChar.ReplaceAllStringFunc(s, manifestEscapeFunc)