1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: Apache-2.0
22 var maxBlockSize = 1 << 26
24 type fsBackend interface {
29 // Ideally *Client would do everything; meanwhile keepBackend
30 // implements fsBackend by merging the two kinds of arvados client.
31 type keepBackend struct {
36 type keepClient interface {
37 ReadAt(locator string, p []byte, off int) (int, error)
38 PutB(p []byte) (string, int, error)
41 type apiClient interface {
42 RequestAndDecode(dst interface{}, method, path string, body io.Reader, params interface{}) error
43 UpdateBody(rsc resource) io.Reader
46 // A CollectionFileSystem is a FileSystem that can be serialized as a
47 // manifest and stored as a collection.
48 type CollectionFileSystem interface {
51 // Flush all file data to Keep and return a snapshot of the
52 // filesystem suitable for saving as (Collection)ManifestText.
53 // Prefix (normally ".") is a top level directory, effectively
54 // prepended to all paths in the returned manifest.
55 MarshalManifest(prefix string) (string, error)
58 // FileSystem returns a CollectionFileSystem for the collection.
59 func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFileSystem, error) {
61 if c.ModifiedAt == nil {
64 modTime = *c.ModifiedAt
66 fs := &collectionFileSystem{
68 fileSystem: fileSystem{
69 fsBackend: keepBackend{apiClient: client, keepClient: kc},
77 mode: os.ModeDir | 0755,
80 inodes: make(map[string]inode),
84 if err := root.loadManifest(c.ManifestText); err != nil {
91 type collectionFileSystem struct {
96 func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime time.Time) (node inode, err error) {
97 if name == "" || name == "." || name == ".." {
98 return nil, ErrInvalidArgument
106 mode: perm | os.ModeDir,
109 inodes: make(map[string]inode),
117 mode: perm & ^os.ModeDir,
124 func (fs *collectionFileSystem) Sync() error {
125 log.Printf("cfs.Sync()")
129 txt, err := fs.MarshalManifest(".")
131 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
138 err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, fs.UpdateBody(coll), map[string]interface{}{"select": []string{"uuid"}})
140 log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err)
145 func (dn *dirnode) Child(name string, replace func(inode) inode) inode {
146 if dn == dn.fs.rootnode() && name == ".arvados#collection" {
147 gn := &getternode{Getter: func() ([]byte, error) {
150 coll.ManifestText, err = dn.fs.MarshalManifest(".")
154 data, err := json.Marshal(&coll)
156 data = append(data, 10)
163 return dn.treenode.Child(name, replace)
166 func (fs *collectionFileSystem) MarshalManifest(prefix string) (string, error) {
167 fs.fileSystem.root.Lock()
168 defer fs.fileSystem.root.Unlock()
169 return fs.fileSystem.root.(*dirnode).marshalManifest(prefix)
172 // filenodePtr is an offset into a file that is (usually) efficient to
173 // seek to. Specifically, if filenode.repacked==filenodePtr.repacked
175 // filenode.segments[filenodePtr.segmentIdx][filenodePtr.segmentOff]
176 // corresponds to file offset filenodePtr.off. Otherwise, it is
177 // necessary to reexamine len(filenode.segments[0]) etc. to find the
178 // correct segment and offset.
179 type filenodePtr struct {
186 // seek returns a ptr that is consistent with both startPtr.off and
187 // the current state of fn. The caller must already hold fn.RLock() or
190 // If startPtr is beyond EOF, ptr.segment* will indicate precisely
195 // ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
197 // filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
198 func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
201 // meaningless anyway
203 } else if ptr.off >= fn.fileinfo.size {
204 ptr.segmentIdx = len(fn.segments)
206 ptr.repacked = fn.repacked
208 } else if ptr.repacked == fn.repacked {
209 // segmentIdx and segmentOff accurately reflect
210 // ptr.off, but might have fallen off the end of a
212 if ptr.segmentOff >= fn.segments[ptr.segmentIdx].Len() {
219 ptr.repacked = fn.repacked
221 if ptr.off >= fn.fileinfo.size {
222 ptr.segmentIdx, ptr.segmentOff = len(fn.segments), 0
225 // Recompute segmentIdx and segmentOff. We have already
226 // established fn.fileinfo.size > ptr.off >= 0, so we don't
227 // have to deal with edge cases here.
229 for ptr.segmentIdx, ptr.segmentOff = 0, 0; off < ptr.off; ptr.segmentIdx++ {
230 // This would panic (index out of range) if
231 // fn.fileinfo.size were larger than
232 // sum(fn.segments[i].Len()) -- but that can't happen
233 // because we have ensured fn.fileinfo.size is always
235 segLen := int64(fn.segments[ptr.segmentIdx].Len())
236 if off+segLen > ptr.off {
237 ptr.segmentOff = int(ptr.off - off)
245 // filenode implements inode.
246 type filenode struct {
251 // number of times `segments` has changed in a
252 // way that might invalidate a filenodePtr
254 memsize int64 // bytes in memSegments
259 // caller must have lock
260 func (fn *filenode) appendSegment(e segment) {
261 fn.segments = append(fn.segments, e)
262 fn.fileinfo.size += int64(e.Len())
265 func (fn *filenode) SetParent(p inode) {
271 func (fn *filenode) Parent() inode {
277 func (fn *filenode) FS() FileSystem {
281 // Read reads file data from a single segment, starting at startPtr,
282 // into p. startPtr is assumed not to be up-to-date. Caller must have
284 func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
285 ptr = fn.seek(startPtr)
287 err = ErrNegativeOffset
290 if ptr.segmentIdx >= len(fn.segments) {
294 n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
298 if ptr.segmentOff == fn.segments[ptr.segmentIdx].Len() {
301 if ptr.segmentIdx < len(fn.segments) && err == io.EOF {
309 func (fn *filenode) Size() int64 {
312 return fn.fileinfo.Size()
315 func (fn *filenode) FileInfo() os.FileInfo {
321 func (fn *filenode) Truncate(size int64) error {
324 return fn.truncate(size)
327 func (fn *filenode) truncate(size int64) error {
328 if size == fn.fileinfo.size {
332 if size < fn.fileinfo.size {
333 ptr := fn.seek(filenodePtr{off: size})
334 for i := ptr.segmentIdx; i < len(fn.segments); i++ {
335 if seg, ok := fn.segments[i].(*memSegment); ok {
336 fn.memsize -= int64(seg.Len())
339 if ptr.segmentOff == 0 {
340 fn.segments = fn.segments[:ptr.segmentIdx]
342 fn.segments = fn.segments[:ptr.segmentIdx+1]
343 switch seg := fn.segments[ptr.segmentIdx].(type) {
345 seg.Truncate(ptr.segmentOff)
346 fn.memsize += int64(seg.Len())
348 fn.segments[ptr.segmentIdx] = seg.Slice(0, ptr.segmentOff)
351 fn.fileinfo.size = size
354 for size > fn.fileinfo.size {
355 grow := size - fn.fileinfo.size
358 if len(fn.segments) == 0 {
360 fn.segments = append(fn.segments, seg)
361 } else if seg, ok = fn.segments[len(fn.segments)-1].(*memSegment); !ok || seg.Len() >= maxBlockSize {
363 fn.segments = append(fn.segments, seg)
365 if maxgrow := int64(maxBlockSize - seg.Len()); maxgrow < grow {
368 seg.Truncate(seg.Len() + int(grow))
369 fn.fileinfo.size += grow
375 // Write writes data from p to the file, starting at startPtr,
376 // extending the file size if necessary. Caller must have Lock.
377 func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
378 if startPtr.off > fn.fileinfo.size {
379 if err = fn.truncate(startPtr.off); err != nil {
380 return 0, startPtr, err
383 ptr = fn.seek(startPtr)
385 err = ErrNegativeOffset
388 for len(p) > 0 && err == nil {
390 if len(cando) > maxBlockSize {
391 cando = cando[:maxBlockSize]
393 // Rearrange/grow fn.segments (and shrink cando if
394 // needed) such that cando can be copied to
395 // fn.segments[ptr.segmentIdx] at offset
397 cur := ptr.segmentIdx
398 prev := ptr.segmentIdx - 1
400 if cur < len(fn.segments) {
401 _, curWritable = fn.segments[cur].(*memSegment)
403 var prevAppendable bool
404 if prev >= 0 && fn.segments[prev].Len() < maxBlockSize {
405 _, prevAppendable = fn.segments[prev].(*memSegment)
407 if ptr.segmentOff > 0 && !curWritable {
408 // Split a non-writable block.
409 if max := fn.segments[cur].Len() - ptr.segmentOff; max <= len(cando) {
410 // Truncate cur, and insert a new
413 fn.segments = append(fn.segments, nil)
414 copy(fn.segments[cur+1:], fn.segments[cur:])
416 // Split cur into two copies, truncate
417 // the one on the left, shift the one
418 // on the right, and insert a new
419 // segment between them.
420 fn.segments = append(fn.segments, nil, nil)
421 copy(fn.segments[cur+2:], fn.segments[cur:])
422 fn.segments[cur+2] = fn.segments[cur+2].Slice(ptr.segmentOff+len(cando), -1)
427 seg.Truncate(len(cando))
428 fn.memsize += int64(len(cando))
429 fn.segments[cur] = seg
430 fn.segments[prev] = fn.segments[prev].Slice(0, ptr.segmentOff)
435 } else if curWritable {
436 if fit := int(fn.segments[cur].Len()) - ptr.segmentOff; fit < len(cando) {
441 // Shrink cando if needed to fit in
443 if cangrow := maxBlockSize - fn.segments[prev].Len(); cangrow < len(cando) {
444 cando = cando[:cangrow]
448 if cur == len(fn.segments) {
449 // ptr is at EOF, filesize is changing.
450 fn.fileinfo.size += int64(len(cando))
451 } else if el := fn.segments[cur].Len(); el <= len(cando) {
452 // cando is long enough that we won't
453 // need cur any more. shrink cando to
454 // be exactly as long as cur
455 // (otherwise we'd accidentally shift
456 // the effective position of all
457 // segments after cur).
459 copy(fn.segments[cur:], fn.segments[cur+1:])
460 fn.segments = fn.segments[:len(fn.segments)-1]
462 // shrink cur by the same #bytes we're growing prev
463 fn.segments[cur] = fn.segments[cur].Slice(len(cando), -1)
469 ptr.segmentOff = fn.segments[prev].Len()
470 fn.segments[prev].(*memSegment).Truncate(ptr.segmentOff + len(cando))
471 fn.memsize += int64(len(cando))
475 // Insert a segment between prev and
476 // cur, and advance prev/cur.
477 fn.segments = append(fn.segments, nil)
478 if cur < len(fn.segments) {
479 copy(fn.segments[cur+1:], fn.segments[cur:])
483 // appending a new segment does
484 // not invalidate any ptrs
487 seg.Truncate(len(cando))
488 fn.memsize += int64(len(cando))
489 fn.segments[cur] = seg
495 // Finally we can copy bytes from cando to the current segment.
496 fn.segments[ptr.segmentIdx].(*memSegment).WriteAt(cando, ptr.segmentOff)
500 ptr.off += int64(len(cando))
501 ptr.segmentOff += len(cando)
502 if ptr.segmentOff >= maxBlockSize {
503 fn.pruneMemSegments()
505 if fn.segments[ptr.segmentIdx].Len() == ptr.segmentOff {
510 fn.fileinfo.modTime = time.Now()
515 // Write some data out to disk to reduce memory use. Caller must have
517 func (fn *filenode) pruneMemSegments() {
518 // TODO: async (don't hold Lock() while waiting for Keep)
519 // TODO: share code with (*dirnode)sync()
520 // TODO: pack/flush small blocks too, when fragmented
521 for idx, seg := range fn.segments {
522 seg, ok := seg.(*memSegment)
523 if !ok || seg.Len() < maxBlockSize {
526 locator, _, err := fn.parent.(fsBackend).PutB(seg.buf)
528 // TODO: stall (or return errors from)
529 // subsequent writes until flushing
533 fn.memsize -= int64(seg.Len())
534 fn.segments[idx] = storedSegment{
544 type dirnode struct {
545 fs *collectionFileSystem
549 func (dn *dirnode) FS() FileSystem {
553 // sync flushes in-memory data (for all files in the tree rooted at
554 // dn) to persistent storage. Caller must hold dn.Lock().
555 func (dn *dirnode) sync() error {
556 type shortBlock struct {
560 var pending []shortBlock
563 flush := func(sbs []shortBlock) error {
567 block := make([]byte, 0, maxBlockSize)
568 for _, sb := range sbs {
569 block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...)
571 locator, _, err := dn.fs.PutB(block)
576 for _, sb := range sbs {
577 data := sb.fn.segments[sb.idx].(*memSegment).buf
578 sb.fn.segments[sb.idx] = storedSegment{
586 sb.fn.memsize -= int64(len(data))
591 names := make([]string, 0, len(dn.inodes))
592 for name := range dn.inodes {
593 names = append(names, name)
597 for _, name := range names {
598 fn, ok := dn.inodes[name].(*filenode)
604 for idx, seg := range fn.segments {
605 seg, ok := seg.(*memSegment)
609 if seg.Len() > maxBlockSize/2 {
610 if err := flush([]shortBlock{{fn, idx}}); err != nil {
615 if pendingLen+seg.Len() > maxBlockSize {
616 if err := flush(pending); err != nil {
622 pending = append(pending, shortBlock{fn, idx})
623 pendingLen += seg.Len()
626 return flush(pending)
629 // caller must have read lock.
630 func (dn *dirnode) marshalManifest(prefix string) (string, error) {
632 type filepart struct {
637 var fileparts []filepart
641 if err := dn.sync(); err != nil {
645 names := make([]string, 0, len(dn.inodes))
646 for name, node := range dn.inodes {
647 names = append(names, name)
653 for _, name := range names {
654 switch node := dn.inodes[name].(type) {
656 subdir, err := node.marshalManifest(prefix + "/" + name)
660 subdirs = subdirs + subdir
662 if len(node.segments) == 0 {
663 fileparts = append(fileparts, filepart{name: name})
666 for _, seg := range node.segments {
667 switch seg := seg.(type) {
669 if len(blocks) > 0 && blocks[len(blocks)-1] == seg.locator {
670 streamLen -= int64(seg.size)
672 blocks = append(blocks, seg.locator)
676 offset: streamLen + int64(seg.offset),
677 length: int64(seg.length),
679 if prev := len(fileparts) - 1; prev >= 0 &&
680 fileparts[prev].name == name &&
681 fileparts[prev].offset+fileparts[prev].length == next.offset {
682 fileparts[prev].length += next.length
684 fileparts = append(fileparts, next)
686 streamLen += int64(seg.size)
688 // This can't happen: we
689 // haven't unlocked since
691 panic(fmt.Sprintf("can't marshal segment type %T", seg))
695 panic(fmt.Sprintf("can't marshal inode type %T", node))
698 var filetokens []string
699 for _, s := range fileparts {
700 filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name)))
702 if len(filetokens) == 0 {
704 } else if len(blocks) == 0 {
705 blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"}
707 return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil
710 func (dn *dirnode) loadManifest(txt string) error {
712 streams := strings.Split(txt, "\n")
713 if streams[len(streams)-1] != "" {
714 return fmt.Errorf("line %d: no trailing newline", len(streams))
716 streams = streams[:len(streams)-1]
717 segments := []storedSegment{}
718 for i, stream := range streams {
720 var anyFileTokens bool
723 segments = segments[:0]
724 for i, token := range strings.Split(stream, " ") {
726 dirname = manifestUnescape(token)
729 if !strings.Contains(token, ":") {
731 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
733 toks := strings.SplitN(token, "+", 3)
735 return fmt.Errorf("line %d: bad locator %q", lineno, token)
737 length, err := strconv.ParseInt(toks[1], 10, 32)
738 if err != nil || length < 0 {
739 return fmt.Errorf("line %d: bad locator %q", lineno, token)
741 segments = append(segments, storedSegment{
748 } else if len(segments) == 0 {
749 return fmt.Errorf("line %d: bad locator %q", lineno, token)
752 toks := strings.SplitN(token, ":", 3)
754 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
758 offset, err := strconv.ParseInt(toks[0], 10, 64)
759 if err != nil || offset < 0 {
760 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
762 length, err := strconv.ParseInt(toks[1], 10, 64)
763 if err != nil || length < 0 {
764 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
766 name := dirname + "/" + manifestUnescape(toks[2])
767 fnode, err := dn.createFileAndParents(name)
769 return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err)
771 // Map the stream offset/range coordinates to
772 // block/offset/range coordinates and add
773 // corresponding storedSegments to the filenode
775 // Can't continue where we left off.
776 // TODO: binary search instead of
777 // rewinding all the way (but this
778 // situation might be rare anyway)
781 for next := int64(0); segIdx < len(segments); segIdx++ {
782 seg := segments[segIdx]
783 next = pos + int64(seg.Len())
784 if next <= offset || seg.Len() == 0 {
788 if pos >= offset+length {
793 blkOff = int(offset - pos)
795 blkLen := seg.Len() - blkOff
796 if pos+int64(blkOff+blkLen) > offset+length {
797 blkLen = int(offset + length - pos - int64(blkOff))
799 fnode.appendSegment(storedSegment{
801 locator: seg.locator,
806 if next > offset+length {
812 if segIdx == len(segments) && pos < offset+length {
813 return fmt.Errorf("line %d: invalid segment in %d-byte stream: %q", lineno, pos, token)
817 return fmt.Errorf("line %d: no file segments", lineno)
818 } else if len(segments) == 0 {
819 return fmt.Errorf("line %d: no locators", lineno)
820 } else if dirname == "" {
821 return fmt.Errorf("line %d: no stream name", lineno)
827 // only safe to call from loadManifest -- no locking
828 func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
830 names := strings.Split(path, "/")
831 basename := names[len(names)-1]
832 if basename == "" || basename == "." || basename == ".." {
833 err = fmt.Errorf("invalid filename")
836 for _, name := range names[:len(names)-1] {
842 // can't be sure parent will be a *dirnode
843 return nil, ErrInvalidArgument
848 node.Child(name, func(child inode) inode {
850 node, err = node.FS().newNode(name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime())
852 } else if !child.IsDir() {
863 node.Child(basename, func(child inode) inode {
864 switch child := child.(type) {
866 child, err = node.FS().newNode(basename, 0755, node.FileInfo().ModTime())
867 fn = child.(*filenode)
876 err = ErrInvalidArgument
883 type segment interface {
886 // Return a new segment with a subsection of the data from this
887 // one. length<0 means length=Len()-off.
888 Slice(off int, length int) segment
891 type memSegment struct {
895 func (me *memSegment) Len() int {
899 func (me *memSegment) Slice(off, length int) segment {
901 length = len(me.buf) - off
903 buf := make([]byte, length)
904 copy(buf, me.buf[off:])
905 return &memSegment{buf: buf}
908 func (me *memSegment) Truncate(n int) {
912 newsize = newsize << 2
914 newbuf := make([]byte, n, newsize)
918 // Zero unused part when shrinking, in case we grow
919 // and start using it again later.
920 for i := n; i < len(me.buf); i++ {
927 func (me *memSegment) WriteAt(p []byte, off int) {
928 if off+len(p) > len(me.buf) {
929 panic("overflowed segment")
931 copy(me.buf[off:], p)
934 func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
935 if off > int64(me.Len()) {
939 n = copy(p, me.buf[int(off):])
946 type storedSegment struct {
949 size int // size of stored block (also encoded in locator)
950 offset int // position of segment within the stored block
951 length int // bytes in this segment (offset + length <= size)
954 func (se storedSegment) Len() int {
958 func (se storedSegment) Slice(n, size int) segment {
961 if size >= 0 && se.length > size {
967 func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
968 if off > int64(se.length) {
971 maxlen := se.length - int(off)
974 n, err = se.kc.ReadAt(se.locator, p, int(off)+se.offset)
980 return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
983 func canonicalName(name string) string {
984 name = path.Clean("/" + name)
985 if name == "/" || name == "./" {
987 } else if strings.HasPrefix(name, "/") {
993 var manifestEscapeSeq = regexp.MustCompile(`\\([0-7]{3}|\\)`)
995 func manifestUnescapeFunc(seq string) string {
999 i, err := strconv.ParseUint(seq[1:], 8, 8)
1001 // Invalid escape sequence: can't unescape.
1004 return string([]byte{byte(i)})
1007 func manifestUnescape(s string) string {
1008 return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeFunc)
1011 var manifestEscapedChar = regexp.MustCompile(`[\000-\040:\s\\]`)
1013 func manifestEscapeFunc(seq string) string {
1014 return fmt.Sprintf("\\%03o", byte(seq[0]))
1017 func manifestEscape(s string) string {
1018 return manifestEscapedChar.ReplaceAllStringFunc(s, manifestEscapeFunc)