1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: Apache-2.0
21 var maxBlockSize = 1 << 26
23 type keepClient interface {
24 ReadAt(locator string, p []byte, off int) (int, error)
25 PutB(p []byte) (string, int, error)
28 // A CollectionFileSystem is a FileSystem that can be serialized as a
29 // manifest and stored as a collection.
30 type CollectionFileSystem interface {
33 // Flush all file data to Keep and return a snapshot of the
34 // filesystem suitable for saving as (Collection)ManifestText.
35 // Prefix (normally ".") is a top level directory, effectively
36 // prepended to all paths in the returned manifest.
37 MarshalManifest(prefix string) (string, error)
40 // FileSystem returns a CollectionFileSystem for the collection.
41 func (c *Collection) FileSystem(client *Client, kc keepClient) (CollectionFileSystem, error) {
43 if c.ModifiedAt == nil {
46 modTime = *c.ModifiedAt
54 mode: os.ModeDir | 0755,
58 inodes: make(map[string]inode),
62 fs := &collectionFileSystem{fileSystem: fileSystem{inode: dn}}
63 if err := dn.loadManifest(c.ManifestText); err != nil {
69 type collectionFileSystem struct {
73 func (fs collectionFileSystem) Child(name string, replace func(inode) inode) inode {
74 if name == ".arvados#collection" {
75 return &getternode{Getter: func() ([]byte, error) {
78 coll.ManifestText, err = fs.MarshalManifest(".")
82 data, err := json.Marshal(&coll)
84 data = append(data, 10)
89 return fs.fileSystem.Child(name, replace)
92 func (fs collectionFileSystem) MarshalManifest(prefix string) (string, error) {
93 fs.fileSystem.inode.Lock()
94 defer fs.fileSystem.inode.Unlock()
95 return fs.fileSystem.inode.(*dirnode).marshalManifest(prefix)
98 // filenodePtr is an offset into a file that is (usually) efficient to
99 // seek to. Specifically, if filenode.repacked==filenodePtr.repacked
101 // filenode.segments[filenodePtr.segmentIdx][filenodePtr.segmentOff]
102 // corresponds to file offset filenodePtr.off. Otherwise, it is
103 // necessary to reexamine len(filenode.segments[0]) etc. to find the
104 // correct segment and offset.
105 type filenodePtr struct {
112 // seek returns a ptr that is consistent with both startPtr.off and
113 // the current state of fn. The caller must already hold fn.RLock() or
116 // If startPtr is beyond EOF, ptr.segment* will indicate precisely
121 // ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
123 // filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
124 func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
127 // meaningless anyway
129 } else if ptr.off >= fn.fileinfo.size {
130 ptr.segmentIdx = len(fn.segments)
132 ptr.repacked = fn.repacked
134 } else if ptr.repacked == fn.repacked {
135 // segmentIdx and segmentOff accurately reflect
136 // ptr.off, but might have fallen off the end of a
138 if ptr.segmentOff >= fn.segments[ptr.segmentIdx].Len() {
145 ptr.repacked = fn.repacked
147 if ptr.off >= fn.fileinfo.size {
148 ptr.segmentIdx, ptr.segmentOff = len(fn.segments), 0
151 // Recompute segmentIdx and segmentOff. We have already
152 // established fn.fileinfo.size > ptr.off >= 0, so we don't
153 // have to deal with edge cases here.
155 for ptr.segmentIdx, ptr.segmentOff = 0, 0; off < ptr.off; ptr.segmentIdx++ {
156 // This would panic (index out of range) if
157 // fn.fileinfo.size were larger than
158 // sum(fn.segments[i].Len()) -- but that can't happen
159 // because we have ensured fn.fileinfo.size is always
161 segLen := int64(fn.segments[ptr.segmentIdx].Len())
162 if off+segLen > ptr.off {
163 ptr.segmentOff = int(ptr.off - off)
171 // filenode implements inode.
172 type filenode struct {
176 // number of times `segments` has changed in a
177 // way that might invalidate a filenodePtr
179 memsize int64 // bytes in memSegments
184 // caller must have lock
185 func (fn *filenode) appendSegment(e segment) {
186 fn.segments = append(fn.segments, e)
187 fn.fileinfo.size += int64(e.Len())
190 func (fn *filenode) Parent() inode {
196 // Read reads file data from a single segment, starting at startPtr,
197 // into p. startPtr is assumed not to be up-to-date. Caller must have
199 func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
200 ptr = fn.seek(startPtr)
202 err = ErrNegativeOffset
205 if ptr.segmentIdx >= len(fn.segments) {
209 n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
213 if ptr.segmentOff == fn.segments[ptr.segmentIdx].Len() {
216 if ptr.segmentIdx < len(fn.segments) && err == io.EOF {
224 func (fn *filenode) Size() int64 {
227 return fn.fileinfo.Size()
230 func (fn *filenode) FileInfo() os.FileInfo {
236 func (fn *filenode) Truncate(size int64) error {
239 return fn.truncate(size)
242 func (fn *filenode) truncate(size int64) error {
243 if size == fn.fileinfo.size {
247 if size < fn.fileinfo.size {
248 ptr := fn.seek(filenodePtr{off: size})
249 for i := ptr.segmentIdx; i < len(fn.segments); i++ {
250 if seg, ok := fn.segments[i].(*memSegment); ok {
251 fn.memsize -= int64(seg.Len())
254 if ptr.segmentOff == 0 {
255 fn.segments = fn.segments[:ptr.segmentIdx]
257 fn.segments = fn.segments[:ptr.segmentIdx+1]
258 switch seg := fn.segments[ptr.segmentIdx].(type) {
260 seg.Truncate(ptr.segmentOff)
261 fn.memsize += int64(seg.Len())
263 fn.segments[ptr.segmentIdx] = seg.Slice(0, ptr.segmentOff)
266 fn.fileinfo.size = size
269 for size > fn.fileinfo.size {
270 grow := size - fn.fileinfo.size
273 if len(fn.segments) == 0 {
275 fn.segments = append(fn.segments, seg)
276 } else if seg, ok = fn.segments[len(fn.segments)-1].(*memSegment); !ok || seg.Len() >= maxBlockSize {
278 fn.segments = append(fn.segments, seg)
280 if maxgrow := int64(maxBlockSize - seg.Len()); maxgrow < grow {
283 seg.Truncate(seg.Len() + int(grow))
284 fn.fileinfo.size += grow
290 // Write writes data from p to the file, starting at startPtr,
291 // extending the file size if necessary. Caller must have Lock.
292 func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
293 if startPtr.off > fn.fileinfo.size {
294 if err = fn.truncate(startPtr.off); err != nil {
295 return 0, startPtr, err
298 ptr = fn.seek(startPtr)
300 err = ErrNegativeOffset
303 for len(p) > 0 && err == nil {
305 if len(cando) > maxBlockSize {
306 cando = cando[:maxBlockSize]
308 // Rearrange/grow fn.segments (and shrink cando if
309 // needed) such that cando can be copied to
310 // fn.segments[ptr.segmentIdx] at offset
312 cur := ptr.segmentIdx
313 prev := ptr.segmentIdx - 1
315 if cur < len(fn.segments) {
316 _, curWritable = fn.segments[cur].(*memSegment)
318 var prevAppendable bool
319 if prev >= 0 && fn.segments[prev].Len() < maxBlockSize {
320 _, prevAppendable = fn.segments[prev].(*memSegment)
322 if ptr.segmentOff > 0 && !curWritable {
323 // Split a non-writable block.
324 if max := fn.segments[cur].Len() - ptr.segmentOff; max <= len(cando) {
325 // Truncate cur, and insert a new
328 fn.segments = append(fn.segments, nil)
329 copy(fn.segments[cur+1:], fn.segments[cur:])
331 // Split cur into two copies, truncate
332 // the one on the left, shift the one
333 // on the right, and insert a new
334 // segment between them.
335 fn.segments = append(fn.segments, nil, nil)
336 copy(fn.segments[cur+2:], fn.segments[cur:])
337 fn.segments[cur+2] = fn.segments[cur+2].Slice(ptr.segmentOff+len(cando), -1)
342 seg.Truncate(len(cando))
343 fn.memsize += int64(len(cando))
344 fn.segments[cur] = seg
345 fn.segments[prev] = fn.segments[prev].Slice(0, ptr.segmentOff)
350 } else if curWritable {
351 if fit := int(fn.segments[cur].Len()) - ptr.segmentOff; fit < len(cando) {
356 // Shrink cando if needed to fit in
358 if cangrow := maxBlockSize - fn.segments[prev].Len(); cangrow < len(cando) {
359 cando = cando[:cangrow]
363 if cur == len(fn.segments) {
364 // ptr is at EOF, filesize is changing.
365 fn.fileinfo.size += int64(len(cando))
366 } else if el := fn.segments[cur].Len(); el <= len(cando) {
367 // cando is long enough that we won't
368 // need cur any more. shrink cando to
369 // be exactly as long as cur
370 // (otherwise we'd accidentally shift
371 // the effective position of all
372 // segments after cur).
374 copy(fn.segments[cur:], fn.segments[cur+1:])
375 fn.segments = fn.segments[:len(fn.segments)-1]
377 // shrink cur by the same #bytes we're growing prev
378 fn.segments[cur] = fn.segments[cur].Slice(len(cando), -1)
384 ptr.segmentOff = fn.segments[prev].Len()
385 fn.segments[prev].(*memSegment).Truncate(ptr.segmentOff + len(cando))
386 fn.memsize += int64(len(cando))
390 // Insert a segment between prev and
391 // cur, and advance prev/cur.
392 fn.segments = append(fn.segments, nil)
393 if cur < len(fn.segments) {
394 copy(fn.segments[cur+1:], fn.segments[cur:])
398 // appending a new segment does
399 // not invalidate any ptrs
402 seg.Truncate(len(cando))
403 fn.memsize += int64(len(cando))
404 fn.segments[cur] = seg
410 // Finally we can copy bytes from cando to the current segment.
411 fn.segments[ptr.segmentIdx].(*memSegment).WriteAt(cando, ptr.segmentOff)
415 ptr.off += int64(len(cando))
416 ptr.segmentOff += len(cando)
417 if ptr.segmentOff >= maxBlockSize {
418 fn.pruneMemSegments()
420 if fn.segments[ptr.segmentIdx].Len() == ptr.segmentOff {
425 fn.fileinfo.modTime = time.Now()
430 // Write some data out to disk to reduce memory use. Caller must have
432 func (fn *filenode) pruneMemSegments() {
433 // TODO: async (don't hold Lock() while waiting for Keep)
434 // TODO: share code with (*dirnode)sync()
435 // TODO: pack/flush small blocks too, when fragmented
436 for idx, seg := range fn.segments {
437 seg, ok := seg.(*memSegment)
438 if !ok || seg.Len() < maxBlockSize {
441 locator, _, err := fn.parent.kc.PutB(seg.buf)
443 // TODO: stall (or return errors from)
444 // subsequent writes until flushing
448 fn.memsize -= int64(seg.Len())
449 fn.segments[idx] = storedSegment{
459 type dirnode struct {
465 // sync flushes in-memory data (for all files in the tree rooted at
466 // dn) to persistent storage. Caller must hold dn.Lock().
467 func (dn *dirnode) sync() error {
468 type shortBlock struct {
472 var pending []shortBlock
475 flush := func(sbs []shortBlock) error {
479 block := make([]byte, 0, maxBlockSize)
480 for _, sb := range sbs {
481 block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...)
483 locator, _, err := dn.kc.PutB(block)
488 for _, sb := range sbs {
489 data := sb.fn.segments[sb.idx].(*memSegment).buf
490 sb.fn.segments[sb.idx] = storedSegment{
498 sb.fn.memsize -= int64(len(data))
503 names := make([]string, 0, len(dn.inodes))
504 for name := range dn.inodes {
505 names = append(names, name)
509 for _, name := range names {
510 fn, ok := dn.inodes[name].(*filenode)
516 for idx, seg := range fn.segments {
517 seg, ok := seg.(*memSegment)
521 if seg.Len() > maxBlockSize/2 {
522 if err := flush([]shortBlock{{fn, idx}}); err != nil {
527 if pendingLen+seg.Len() > maxBlockSize {
528 if err := flush(pending); err != nil {
534 pending = append(pending, shortBlock{fn, idx})
535 pendingLen += seg.Len()
538 return flush(pending)
541 // caller must have read lock.
542 func (dn *dirnode) marshalManifest(prefix string) (string, error) {
544 type filepart struct {
549 var fileparts []filepart
553 if err := dn.sync(); err != nil {
557 names := make([]string, 0, len(dn.inodes))
558 for name, node := range dn.inodes {
559 names = append(names, name)
565 for _, name := range names {
566 switch node := dn.inodes[name].(type) {
568 subdir, err := node.marshalManifest(prefix + "/" + name)
572 subdirs = subdirs + subdir
574 if len(node.segments) == 0 {
575 fileparts = append(fileparts, filepart{name: name})
578 for _, seg := range node.segments {
579 switch seg := seg.(type) {
581 if len(blocks) > 0 && blocks[len(blocks)-1] == seg.locator {
582 streamLen -= int64(seg.size)
584 blocks = append(blocks, seg.locator)
588 offset: streamLen + int64(seg.offset),
589 length: int64(seg.length),
591 if prev := len(fileparts) - 1; prev >= 0 &&
592 fileparts[prev].name == name &&
593 fileparts[prev].offset+fileparts[prev].length == next.offset {
594 fileparts[prev].length += next.length
596 fileparts = append(fileparts, next)
598 streamLen += int64(seg.size)
600 // This can't happen: we
601 // haven't unlocked since
603 panic(fmt.Sprintf("can't marshal segment type %T", seg))
607 panic(fmt.Sprintf("can't marshal inode type %T", node))
610 var filetokens []string
611 for _, s := range fileparts {
612 filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name)))
614 if len(filetokens) == 0 {
616 } else if len(blocks) == 0 {
617 blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"}
619 return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil
622 func (dn *dirnode) loadManifest(txt string) error {
624 streams := strings.Split(txt, "\n")
625 if streams[len(streams)-1] != "" {
626 return fmt.Errorf("line %d: no trailing newline", len(streams))
628 streams = streams[:len(streams)-1]
629 segments := []storedSegment{}
630 for i, stream := range streams {
632 var anyFileTokens bool
635 segments = segments[:0]
636 for i, token := range strings.Split(stream, " ") {
638 dirname = manifestUnescape(token)
641 if !strings.Contains(token, ":") {
643 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
645 toks := strings.SplitN(token, "+", 3)
647 return fmt.Errorf("line %d: bad locator %q", lineno, token)
649 length, err := strconv.ParseInt(toks[1], 10, 32)
650 if err != nil || length < 0 {
651 return fmt.Errorf("line %d: bad locator %q", lineno, token)
653 segments = append(segments, storedSegment{
660 } else if len(segments) == 0 {
661 return fmt.Errorf("line %d: bad locator %q", lineno, token)
664 toks := strings.SplitN(token, ":", 3)
666 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
670 offset, err := strconv.ParseInt(toks[0], 10, 64)
671 if err != nil || offset < 0 {
672 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
674 length, err := strconv.ParseInt(toks[1], 10, 64)
675 if err != nil || length < 0 {
676 return fmt.Errorf("line %d: bad file segment %q", lineno, token)
678 name := dirname + "/" + manifestUnescape(toks[2])
679 fnode, err := dn.createFileAndParents(name)
681 return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err)
683 // Map the stream offset/range coordinates to
684 // block/offset/range coordinates and add
685 // corresponding storedSegments to the filenode
687 // Can't continue where we left off.
688 // TODO: binary search instead of
689 // rewinding all the way (but this
690 // situation might be rare anyway)
693 for next := int64(0); segIdx < len(segments); segIdx++ {
694 seg := segments[segIdx]
695 next = pos + int64(seg.Len())
696 if next <= offset || seg.Len() == 0 {
700 if pos >= offset+length {
705 blkOff = int(offset - pos)
707 blkLen := seg.Len() - blkOff
708 if pos+int64(blkOff+blkLen) > offset+length {
709 blkLen = int(offset + length - pos - int64(blkOff))
711 fnode.appendSegment(storedSegment{
713 locator: seg.locator,
718 if next > offset+length {
724 if segIdx == len(segments) && pos < offset+length {
725 return fmt.Errorf("line %d: invalid segment in %d-byte stream: %q", lineno, pos, token)
729 return fmt.Errorf("line %d: no file segments", lineno)
730 } else if len(segments) == 0 {
731 return fmt.Errorf("line %d: no locators", lineno)
732 } else if dirname == "" {
733 return fmt.Errorf("line %d: no stream name", lineno)
739 // only safe to call from loadManifest -- no locking
740 func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
742 names := strings.Split(path, "/")
743 basename := names[len(names)-1]
744 if basename == "" || basename == "." || basename == ".." {
745 err = fmt.Errorf("invalid filename")
748 for _, name := range names[:len(names)-1] {
754 // can't be sure parent will be a *dirnode
755 return nil, ErrInvalidArgument
757 node = node.Parent().(*dirnode)
760 node.Child(name, func(child inode) inode {
761 switch child.(type) {
763 node, err = dn.newDirnode(node, name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime())
766 node = child.(*dirnode)
770 err = ErrInvalidOperation
778 node.Child(basename, func(child inode) inode {
779 switch child := child.(type) {
781 fn, err = dn.newFilenode(node, basename, 0755, node.FileInfo().ModTime())
790 err = ErrInvalidOperation
797 // rlookup (recursive lookup) returns the inode for the file/directory
798 // with the given name (which may contain "/" separators). If no such
799 // file/directory exists, the returned node is nil.
800 func rlookup(start inode, path string) (node inode) {
802 for _, name := range strings.Split(path, "/") {
807 if name == "." || name == "" {
815 node = func() inode {
818 return node.Child(name, nil)
824 // Caller must have lock, and must have already ensured
825 // Children(name,nil) is nil.
826 func (dn *dirnode) newDirnode(parent *dirnode, name string, perm os.FileMode, modTime time.Time) (node *dirnode, err error) {
827 if name == "" || name == "." || name == ".." {
828 return nil, ErrInvalidArgument
837 mode: perm | os.ModeDir,
840 inodes: make(map[string]inode),
845 func (dn *dirnode) newFilenode(parent *dirnode, name string, perm os.FileMode, modTime time.Time) (node *filenode, err error) {
846 if name == "" || name == "." || name == ".." {
847 return nil, ErrInvalidArgument
853 mode: perm & ^os.ModeDir,
859 type segment interface {
862 // Return a new segment with a subsection of the data from this
863 // one. length<0 means length=Len()-off.
864 Slice(off int, length int) segment
867 type memSegment struct {
871 func (me *memSegment) Len() int {
875 func (me *memSegment) Slice(off, length int) segment {
877 length = len(me.buf) - off
879 buf := make([]byte, length)
880 copy(buf, me.buf[off:])
881 return &memSegment{buf: buf}
884 func (me *memSegment) Truncate(n int) {
888 newsize = newsize << 2
890 newbuf := make([]byte, n, newsize)
894 // Zero unused part when shrinking, in case we grow
895 // and start using it again later.
896 for i := n; i < len(me.buf); i++ {
903 func (me *memSegment) WriteAt(p []byte, off int) {
904 if off+len(p) > len(me.buf) {
905 panic("overflowed segment")
907 copy(me.buf[off:], p)
910 func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
911 if off > int64(me.Len()) {
915 n = copy(p, me.buf[int(off):])
922 type storedSegment struct {
925 size int // size of stored block (also encoded in locator)
926 offset int // position of segment within the stored block
927 length int // bytes in this segment (offset + length <= size)
930 func (se storedSegment) Len() int {
934 func (se storedSegment) Slice(n, size int) segment {
937 if size >= 0 && se.length > size {
943 func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
944 if off > int64(se.length) {
947 maxlen := se.length - int(off)
950 n, err = se.kc.ReadAt(se.locator, p, int(off)+se.offset)
956 return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
959 func canonicalName(name string) string {
960 name = path.Clean("/" + name)
961 if name == "/" || name == "./" {
963 } else if strings.HasPrefix(name, "/") {
969 var manifestEscapeSeq = regexp.MustCompile(`\\([0-7]{3}|\\)`)
971 func manifestUnescapeFunc(seq string) string {
975 i, err := strconv.ParseUint(seq[1:], 8, 8)
977 // Invalid escape sequence: can't unescape.
980 return string([]byte{byte(i)})
983 func manifestUnescape(s string) string {
984 return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeFunc)
987 var manifestEscapedChar = regexp.MustCompile(`[\000-\040:\s\\]`)
989 func manifestEscapeFunc(seq string) string {
990 return fmt.Sprintf("\\%03o", byte(seq[0]))
993 func manifestEscape(s string) string {
994 return manifestEscapedChar.ReplaceAllStringFunc(s, manifestEscapeFunc)