X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3f38a38ae453390856b3d5cf2b4d5705df06ee13..c502c5a50aae825683ee4cff629c6839a4209501:/sdk/go/arvados/fs_collection.go

diff --git a/sdk/go/arvados/fs_collection.go b/sdk/go/arvados/fs_collection.go
index 4d9db421fc..d3af92f9e1 100644
--- a/sdk/go/arvados/fs_collection.go
+++ b/sdk/go/arvados/fs_collection.go
@@ -5,6 +5,7 @@
 package arvados
 
 import (
+	"bytes"
 	"context"
 	"encoding/json"
 	"fmt"
@@ -43,8 +44,20 @@ type CollectionFileSystem interface {
 type collectionFileSystem struct {
 	fileSystem
 	uuid           string
+	savedPDH       atomic.Value
 	replicas       int
 	storageClasses []string
+	// guessSignatureTTL tracks a lower bound for the server's
+	// configured BlobSigningTTL. The guess is initially zero, and
+	// increases when we come across a signature with an expiry
+	// time further in the future than the previous guess.
+	//
+	// When the guessed TTL is much smaller than the real TTL,
+	// preemptive signature refresh is delayed or missed entirely,
+	// which is OK.
+	guessSignatureTTL time.Duration
+	holdCheckChanges  time.Time
+	lockCheckChanges  sync.Mutex
 }
 
 // FileSystem returns a CollectionFileSystem for the collection.
@@ -61,6 +74,7 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile
 			thr:       newThrottle(concurrentWriters),
 		},
 	}
+	fs.savedPDH.Store(c.PortableDataHash)
 	if r := c.ReplicationDesired; r != nil {
 		fs.replicas = *r
 	}
@@ -71,6 +85,7 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile
 				name:    ".",
 				mode:    os.ModeDir | 0755,
 				modTime: modTime,
+				sys:     c,
 			},
 			inodes: make(map[string]inode),
 		},
@@ -84,16 +99,112 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile
 	return fs, nil
 }
 
-func backdateTree(n inode, modTime time.Time) {
+// caller must have lock (or guarantee no concurrent accesses somehow)
+func eachNode(n inode, ffunc func(*filenode), dfunc func(*dirnode)) {
 	switch n := n.(type) {
 	case *filenode:
-		n.fileinfo.modTime = modTime
+		if ffunc != nil {
+			ffunc(n)
+		}
 	case *dirnode:
-		n.fileinfo.modTime = modTime
+		if dfunc != nil {
+			dfunc(n)
+		}
 		for _, n := range n.inodes {
-			backdateTree(n, modTime)
+			eachNode(n, ffunc, dfunc)
+		}
+	}
+}
+
+// caller must have lock (or guarantee no concurrent accesses somehow)
+func backdateTree(n inode, modTime time.Time) {
+	eachNode(n, func(fn *filenode) {
+		fn.fileinfo.modTime = modTime
+	}, func(dn *dirnode) {
+		dn.fileinfo.modTime = modTime
+	})
+}
+
+// Approximate portion of signature TTL remaining, usually between 0
+// and 1, or negative if some signatures have expired.
+func (fs *collectionFileSystem) signatureTimeLeft() (float64, time.Duration) {
+	var (
+		now      = time.Now()
+		earliest = now.Add(time.Hour * 24 * 7 * 365)
+		latest   time.Time
+	)
+	fs.fileSystem.root.RLock()
+	eachNode(fs.root, func(fn *filenode) {
+		fn.Lock()
+		defer fn.Unlock()
+		for _, seg := range fn.segments {
+			seg, ok := seg.(storedSegment)
+			if !ok {
+				continue
+			}
+			expiryTime, err := signatureExpiryTime(seg.locator)
+			if err != nil {
+				continue
+			}
+			if expiryTime.Before(earliest) {
+				earliest = expiryTime
+			}
+			if expiryTime.After(latest) {
+				latest = expiryTime
+			}
+		}
+	}, nil)
+	fs.fileSystem.root.RUnlock()
+
+	if latest.IsZero() {
+		// No signatures == 100% of TTL remaining.
+		return 1, 1
+	}
+
+	ttl := latest.Sub(now)
+	fs.fileSystem.root.Lock()
+	{
+		if ttl > fs.guessSignatureTTL {
+			// ttl is closer to the real TTL than
+			// guessSignatureTTL.
+			fs.guessSignatureTTL = ttl
+		} else {
+			// Use the previous best guess to compute the
+			// portion remaining (below, after unlocking
+			// mutex).
+			ttl = fs.guessSignatureTTL
+		}
+	}
+	fs.fileSystem.root.Unlock()
+
+	return earliest.Sub(now).Seconds() / ttl.Seconds(), ttl
+}
+
+func (fs *collectionFileSystem) updateSignatures(newmanifest string) {
+	newLoc := map[string]string{}
+	for _, tok := range regexp.MustCompile(`\S+`).FindAllString(newmanifest, -1) {
+		if mBlkRe.MatchString(tok) {
+			newLoc[stripAllHints(tok)] = tok
 		}
 	}
+	fs.fileSystem.root.Lock()
+	defer fs.fileSystem.root.Unlock()
+	eachNode(fs.root, func(fn *filenode) {
+		fn.Lock()
+		defer fn.Unlock()
+		for idx, seg := range fn.segments {
+			seg, ok := seg.(storedSegment)
+			if !ok {
+				continue
+			}
+			loc, ok := newLoc[stripAllHints(seg.locator)]
+			if !ok {
+				continue
+			}
+			seg.locator = loc
+			fn.segments[idx] = seg
+		}
+	}, nil)
 }
 
 func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime time.Time) (node inode, err error) {
@@ -179,7 +290,88 @@ func (fs *collectionFileSystem) Truncate(int64) error {
 	return ErrInvalidOperation
 }
 
+// Check for and incorporate upstream changes -- unless that has
+// already been done recently, in which case this func is a no-op.
+func (fs *collectionFileSystem) checkChangesOnServer() error {
+	if fs.uuid == "" && fs.savedPDH.Load() == "" {
+		return nil
+	}
+
+	// First try UUID if any, then last known PDH. Stop if all
+	// signatures are new enough.
+	checkingAll := false
+	for _, id := range []string{fs.uuid, fs.savedPDH.Load().(string)} {
+		if id == "" {
+			continue
+		}
+
+		fs.lockCheckChanges.Lock()
+		if !checkingAll && fs.holdCheckChanges.After(time.Now()) {
+			fs.lockCheckChanges.Unlock()
+			return nil
+		}
+		remain, ttl := fs.signatureTimeLeft()
+		if remain > 0.01 && !checkingAll {
+			fs.holdCheckChanges = time.Now().Add(ttl / 100)
+		}
+		fs.lockCheckChanges.Unlock()
+
+		if remain >= 0.5 {
+			break
+		}
+		checkingAll = true
+		var coll Collection
+		err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+id, nil, map[string]interface{}{"select": []string{"portable_data_hash", "manifest_text"}})
+		if err != nil {
+			continue
+		}
+		fs.updateSignatures(coll.ManifestText)
+	}
+	return nil
+}
+
+// Refresh signature on a single locator, if necessary. Assume caller
+// has lock. If an update is needed, and there are any storedSegments
+// whose signatures can be updated, start a background task to update
+// them asynchronously when the caller releases locks.
+func (fs *collectionFileSystem) refreshSignature(locator string) string {
+	exp, err := signatureExpiryTime(locator)
+	if err != nil || exp.Sub(time.Now()) > time.Minute {
+		// Synchronous update is not needed. Start an
+		// asynchronous update if needed.
+		go fs.checkChangesOnServer()
+		return locator
+	}
+	var manifests string
+	for _, id := range []string{fs.uuid, fs.savedPDH.Load().(string)} {
+		if id == "" {
+			continue
+		}
+		var coll Collection
+		err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+id, nil, map[string]interface{}{"select": []string{"portable_data_hash", "manifest_text"}})
+		if err != nil {
+			continue
+		}
+		manifests += coll.ManifestText
+	}
+	hash := stripAllHints(locator)
+	for _, tok := range regexp.MustCompile(`\S+`).FindAllString(manifests, -1) {
+		if mBlkRe.MatchString(tok) {
+			if stripAllHints(tok) == hash {
+				locator = tok
+				break
+			}
+		}
+	}
+	go fs.updateSignatures(manifests)
+	return locator
+}
+
 func (fs *collectionFileSystem) Sync() error {
+	err := fs.checkChangesOnServer()
+	if err != nil {
+		return err
+	}
 	if fs.uuid == "" {
 		return nil
 	}
@@ -187,19 +379,34 @@ func (fs *collectionFileSystem) Sync() error {
 	if err != nil {
 		return fmt.Errorf("sync failed: %s", err)
 	}
-	coll := &Collection{
+	if PortableDataHash(txt) == fs.savedPDH.Load() {
+		// No local changes since last save or initial load.
+		return nil
+	}
+	coll := Collection{
 		UUID:         fs.uuid,
 		ManifestText: txt,
 	}
-	err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, nil, map[string]interface{}{
+
+	selectFields := []string{"uuid", "portable_data_hash"}
+	fs.lockCheckChanges.Lock()
+	remain, _ := fs.signatureTimeLeft()
+	fs.lockCheckChanges.Unlock()
+	if remain < 0.5 {
+		selectFields = append(selectFields, "manifest_text")
+	}
+
+	err = fs.RequestAndDecode(&coll, "PUT", "arvados/v1/collections/"+fs.uuid, nil, map[string]interface{}{
 		"collection": map[string]string{
 			"manifest_text": coll.ManifestText,
 		},
-		"select": []string{"uuid"},
+		"select": selectFields,
 	})
 	if err != nil {
 		return fmt.Errorf("sync failed: update %s: %s", fs.uuid, err)
 	}
+	fs.updateSignatures(coll.ManifestText)
+	fs.savedPDH.Store(coll.PortableDataHash)
 	return nil
 }
 
@@ -251,6 +458,14 @@ func (fs *collectionFileSystem) Size() int64 {
 	return fs.fileSystem.root.(*dirnode).TreeSize()
 }
 
+func (fs *collectionFileSystem) Snapshot() (inode, error) {
+	return fs.fileSystem.root.Snapshot()
+}
+
+func (fs *collectionFileSystem) Splice(r inode) error {
+	return fs.fileSystem.root.Splice(r)
+}
+
 // filenodePtr is an offset into a file that is (usually) efficient to
 // seek to. Specifically, if filenode.repacked==filenodePtr.repacked
 // then
@@ -374,6 +589,10 @@ func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr
 		err = io.EOF
 		return
 	}
+	if ss, ok := fn.segments[ptr.segmentIdx].(storedSegment); ok {
+		ss.locator = fn.fs.refreshSignature(ss.locator)
+		fn.segments[ptr.segmentIdx] = ss
+	}
 	n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff))
 	if n > 0 {
 		ptr.off += int64(n)
@@ -666,6 +885,47 @@ func (fn *filenode) waitPrune() {
 	}
 }
 
+func (fn *filenode) Snapshot() (inode, error) {
+	fn.RLock()
+	defer fn.RUnlock()
+	segments := make([]segment, 0, len(fn.segments))
+	for _, seg := range fn.segments {
+		segments = append(segments, seg.Slice(0, seg.Len()))
+	}
+	return &filenode{
+		fileinfo: fn.fileinfo,
+		segments: segments,
+	}, nil
+}
+
+func (fn *filenode) Splice(repl inode) error {
+	repl, err := repl.Snapshot()
+	if err != nil {
+		return err
+	}
+	fn.parent.Lock()
+	defer fn.parent.Unlock()
+	fn.Lock()
+	defer fn.Unlock()
+	_, err = fn.parent.Child(fn.fileinfo.name, func(inode) (inode, error) { return repl, nil })
+	if err != nil {
+		return err
+	}
+	switch repl := repl.(type) {
+	case *dirnode:
+		repl.parent = fn.parent
+		repl.fileinfo.name = fn.fileinfo.name
+		repl.setTreeFS(fn.fs)
+	case *filenode:
+		repl.parent = fn.parent
+		repl.fileinfo.name = fn.fileinfo.name
+		repl.fs = fn.fs
+	default:
+		return fmt.Errorf("cannot splice snapshot containing %T: %w", repl, ErrInvalidArgument)
+	}
+	return nil
+}
+
 type dirnode struct {
 	fs *collectionFileSystem
 	treenode
@@ -900,15 +1160,17 @@ func (dn *dirnode) MemorySize() (size int64) {
 		case *dirnode:
 			size += node.MemorySize()
 		case *filenode:
+			size += 64
 			for _, seg := range node.segments {
 				switch seg := seg.(type) {
 				case *memSegment:
 					size += int64(seg.Len())
 				}
+				size += 64
 			}
 		}
 	}
-	return
+	return 64 + size
 }
 
 // caller must have write lock.
@@ -1040,38 +1302,64 @@ func (dn *dirnode) marshalManifest(ctx context.Context, prefix string) (string,
 }
 
 func (dn *dirnode) loadManifest(txt string) error {
-	var dirname string
-	streams := strings.Split(txt, "\n")
-	if streams[len(streams)-1] != "" {
+	streams := bytes.Split([]byte(txt), []byte{'\n'})
+	if len(streams[len(streams)-1]) != 0 {
 		return fmt.Errorf("line %d: no trailing newline", len(streams))
 	}
 	streams = streams[:len(streams)-1]
 	segments := []storedSegment{}
+	// To reduce allocs, we reuse a single "pathparts" slice
+	// (pre-split on "/" separators) for the duration of this
+	// func.
+	var pathparts []string
+	// To reduce allocs, we reuse a single "toks" slice of 3 byte
+	// slices.
+	var toks = make([][]byte, 3)
+	// Similar to bytes.SplitN(token, []byte{c}, 3), but splits
+	// into the toks slice rather than allocating a new one, and
+	// returns the number of toks (1, 2, or 3).
+	splitToToks := func(src []byte, c rune) int {
+		c1 := bytes.IndexRune(src, c)
+		if c1 < 0 {
+			toks[0] = src
+			return 1
+		}
+		toks[0], src = src[:c1], src[c1+1:]
+		c2 := bytes.IndexRune(src, c)
+		if c2 < 0 {
+			toks[1] = src
+			return 2
+		}
+		toks[1], toks[2] = src[:c2], src[c2+1:]
+		return 3
+	}
 	for i, stream := range streams {
 		lineno := i + 1
 		var anyFileTokens bool
 		var pos int64
 		var segIdx int
 		segments = segments[:0]
-		for i, token := range strings.Split(stream, " ") {
+		pathparts = nil
+		streamparts := 0
+		for i, token := range bytes.Split(stream, []byte{' '}) {
 			if i == 0 {
-				dirname = manifestUnescape(token)
+				pathparts = strings.Split(manifestUnescape(string(token)), "/")
+				streamparts = len(pathparts)
 				continue
 			}
-			if !strings.Contains(token, ":") {
+			if !bytes.ContainsRune(token, ':') {
 				if anyFileTokens {
 					return fmt.Errorf("line %d: bad file segment %q", lineno, token)
 				}
-				toks := strings.SplitN(token, "+", 3)
-				if len(toks) < 2 {
+				if splitToToks(token, '+') < 2 {
 					return fmt.Errorf("line %d: bad locator %q", lineno, token)
 				}
-				length, err := strconv.ParseInt(toks[1], 10, 32)
+				length, err := strconv.ParseInt(string(toks[1]), 10, 32)
 				if err != nil || length < 0 {
 					return fmt.Errorf("line %d: bad locator %q", lineno, token)
 				}
 				segments = append(segments, storedSegment{
-					locator: token,
+					locator: string(token),
 					size:    int(length),
 					offset:  0,
 					length:  int(length),
@@ -1080,23 +1368,26 @@ func (dn *dirnode) loadManifest(txt string) error {
 			} else if len(segments) == 0 {
 				return fmt.Errorf("line %d: bad locator %q", lineno, token)
 			}
-
-			toks := strings.SplitN(token, ":", 3)
-			if len(toks) != 3 {
+			if splitToToks(token, ':') != 3 {
 				return fmt.Errorf("line %d: bad file segment %q", lineno, token)
 			}
 			anyFileTokens = true
 
-			offset, err := strconv.ParseInt(toks[0], 10, 64)
+			offset, err := strconv.ParseInt(string(toks[0]), 10, 64)
 			if err != nil || offset < 0 {
 				return fmt.Errorf("line %d: bad file segment %q", lineno, token)
 			}
-			length, err := strconv.ParseInt(toks[1], 10, 64)
+			length, err := strconv.ParseInt(string(toks[1]), 10, 64)
 			if err != nil || length < 0 {
 				return fmt.Errorf("line %d: bad file segment %q", lineno, token)
 			}
-			name := dirname + "/" + manifestUnescape(toks[2])
-			fnode, err := dn.createFileAndParents(name)
+			if !bytes.ContainsAny(toks[2], `\/`) {
+				// optimization for a common case
+				pathparts = append(pathparts[:streamparts], string(toks[2]))
+			} else {
+				pathparts = append(pathparts[:streamparts], strings.Split(manifestUnescape(string(toks[2])), "/")...)
+			}
+			fnode, err := dn.createFileAndParents(pathparts)
 			if fnode == nil && err == nil && length == 0 {
 				// Special case: an empty file used as
 				// a marker to preserve an otherwise
@@ -1104,7 +1395,7 @@ func (dn *dirnode) loadManifest(txt string) error {
 				continue
 			}
 			if err != nil || (fnode == nil && length != 0) {
-				return fmt.Errorf("line %d: cannot use path %q with length %d: %s", lineno, name, length, err)
+				return fmt.Errorf("line %d: cannot use name %q with length %d: %s", lineno, toks[2], length, err)
 			}
 			// Map the stream offset/range coordinates to
 			// block/offset/range coordinates and add
@@ -1155,7 +1446,7 @@ func (dn *dirnode) loadManifest(txt string) error {
 			return fmt.Errorf("line %d: no file segments", lineno)
 		} else if len(segments) == 0 {
 			return fmt.Errorf("line %d: no locators", lineno)
-		} else if dirname == "" {
+		} else if streamparts == 0 {
 			return fmt.Errorf("line %d: no stream name", lineno)
 		}
 	}
@@ -1166,9 +1457,11 @@ func (dn *dirnode) loadManifest(txt string) error {
 //
 // If path is a "parent directory exists" marker (the last path
 // component is "."), the returned values are both nil.
-func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
+//
+// Newly added nodes have modtime==0. Caller is responsible for fixing
+// them with backdateTree.
+func (dn *dirnode) createFileAndParents(names []string) (fn *filenode, err error) {
 	var node inode = dn
-	names := strings.Split(path, "/")
 	basename := names[len(names)-1]
 	for _, name := range names[:len(names)-1] {
 		switch name {
@@ -1182,12 +1475,12 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
 			node = node.Parent()
 			continue
 		}
-		modtime := node.Parent().FileInfo().ModTime()
 		node.Lock()
-		locked := node
+		unlock := node.Unlock
 		node, err = node.Child(name, func(child inode) (inode, error) {
 			if child == nil {
-				child, err := node.FS().newNode(name, 0755|os.ModeDir, modtime)
+				// note modtime will be fixed later in backdateTree()
+				child, err := node.FS().newNode(name, 0755|os.ModeDir, time.Time{})
 				if err != nil {
 					return nil, err
 				}
@@ -1199,7 +1492,7 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
 				return child, nil
 			}
 		})
-		locked.Unlock()
+		unlock()
 		if err != nil {
 			return
 		}
@@ -1207,16 +1500,15 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) {
 	if basename == "." {
 		return
 	} else if !permittedName(basename) {
-		err = fmt.Errorf("invalid file part %q in path %q", basename, path)
+		err = fmt.Errorf("invalid file part %q in path %q", basename, names)
 		return
 	}
-	modtime := node.FileInfo().ModTime()
 	node.Lock()
 	defer node.Unlock()
 	_, err = node.Child(basename, func(child inode) (inode, error) {
 		switch child := child.(type) {
 		case nil:
-			child, err = node.FS().newNode(basename, 0755, modtime)
+			child, err = node.FS().newNode(basename, 0755, time.Time{})
 			if err != nil {
 				return nil, err
 			}
@@ -1249,6 +1541,86 @@ func (dn *dirnode) TreeSize() (bytes int64) {
 	return
 }
 
+func (dn *dirnode) Snapshot() (inode, error) {
+	return dn.snapshot()
+}
+
+func (dn *dirnode) snapshot() (*dirnode, error) {
+	dn.RLock()
+	defer dn.RUnlock()
+	snap := &dirnode{
+		treenode: treenode{
+			inodes:   make(map[string]inode, len(dn.inodes)),
+			fileinfo: dn.fileinfo,
+		},
+	}
+	for name, child := range dn.inodes {
+		dupchild, err := child.Snapshot()
+		if err != nil {
+			return nil, err
+		}
+		snap.inodes[name] = dupchild
+		dupchild.SetParent(snap, name)
+	}
+	return snap, nil
+}
+
+func (dn *dirnode) Splice(repl inode) error {
+	repl, err := repl.Snapshot()
+	if err != nil {
+		return fmt.Errorf("cannot copy snapshot: %w", err)
+	}
+	switch repl := repl.(type) {
+	default:
+		return fmt.Errorf("cannot splice snapshot containing %T: %w", repl, ErrInvalidArgument)
+	case *dirnode:
+		dn.Lock()
+		defer dn.Unlock()
+		dn.inodes = repl.inodes
+		dn.setTreeFS(dn.fs)
+	case *filenode:
+		dn.parent.Lock()
+		defer dn.parent.Unlock()
+		removing, err := dn.parent.Child(dn.fileinfo.name, nil)
+		if err != nil {
+			return fmt.Errorf("cannot use Splice to replace a top-level directory with a file: %w", ErrInvalidOperation)
+		} else if removing != dn {
+			// If ../thisdirname is not this dirnode, it
+			// must be an inode that wraps a dirnode, like
+			// a collectionFileSystem or deferrednode.
+			if deferred, ok := removing.(*deferrednode); ok {
+				// More useful to report the type of
+				// the wrapped node rather than just
+				// *deferrednode. (We know the real
+				// inode is already loaded because dn
+				// is inside it.)
+				removing = deferred.realinode()
+			}
+			return fmt.Errorf("cannot use Splice to attach a file at top level of %T: %w", removing, ErrInvalidOperation)
+		}
+		dn.Lock()
+		defer dn.Unlock()
+		_, err = dn.parent.Child(dn.fileinfo.name, func(inode) (inode, error) { return repl, nil })
+		if err != nil {
+			return fmt.Errorf("error replacing filenode: dn.parent.Child(): %w", err)
+		}
+		repl.fs = dn.fs
+	}
+	return nil
+}
+
+func (dn *dirnode) setTreeFS(fs *collectionFileSystem) {
+	dn.fs = fs
+	for _, child := range dn.inodes {
+		switch child := child.(type) {
+		case *dirnode:
+			child.setTreeFS(fs)
+		case *filenode:
+			child.fs = fs
+		}
+	}
+}
+
 type segment interface {
 	io.ReaderAt
 	Len() int