X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c8bf4dc1eef2a73b4b01501eabdc922e2a27a276..c4d1131613de217719929ff05a06f19321cb5fdc:/sdk/go/arvados/fs_collection.go

diff --git a/sdk/go/arvados/fs_collection.go b/sdk/go/arvados/fs_collection.go
index 2b5df76ad6..354658a257 100644
--- a/sdk/go/arvados/fs_collection.go
+++ b/sdk/go/arvados/fs_collection.go
@@ -44,8 +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.
@@ -62,6 +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
 	}
@@ -72,6 +85,7 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile
 				name:    ".",
 				mode:    os.ModeDir | 0755,
 				modTime: modTime,
+				sys:     func() interface{} { return c },
 			},
 			inodes: make(map[string]inode),
 		},
@@ -85,18 +99,114 @@ 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) {
 	if name == "" || name == "." || name == ".." {
 		return nil, ErrInvalidArgument
@@ -180,27 +290,149 @@ func (fs *collectionFileSystem) Truncate(int64) error {
 	return ErrInvalidOperation
 }
 
+// Check for and incorporate upstream changes. If force==false, this
+// is a no-op except once every ttl/100 or so.
+//
+// Return value is true if new content was loaded from upstream and
+// any unsaved local changes have been discarded.
+func (fs *collectionFileSystem) checkChangesOnServer(force bool) (bool, error) {
+	if fs.uuid == "" && fs.savedPDH.Load() == "" {
+		return false, nil
+	}
+
+	fs.lockCheckChanges.Lock()
+	if !force && fs.holdCheckChanges.After(time.Now()) {
+		fs.lockCheckChanges.Unlock()
+		return false, nil
+	}
+	remain, ttl := fs.signatureTimeLeft()
+	if remain > 0.01 {
+		fs.holdCheckChanges = time.Now().Add(ttl / 100)
+	}
+	fs.lockCheckChanges.Unlock()
+
+	if !force && remain >= 0.5 {
+		// plenty of time left on current signatures
+		return false, nil
+	}
+
+	getparams := map[string]interface{}{"select": []string{"portable_data_hash", "manifest_text"}}
+	if fs.uuid != "" {
+		var coll Collection
+		err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+fs.uuid, nil, getparams)
+		if err != nil {
+			return false, err
+		}
+		if coll.PortableDataHash != fs.savedPDH.Load().(string) {
+			// collection has changed upstream since we
+			// last loaded or saved. Refresh local data,
+			// losing any unsaved local changes.
+			newfs, err := coll.FileSystem(fs.fileSystem.fsBackend, fs.fileSystem.fsBackend)
+			if err != nil {
+				return false, err
+			}
+			snap, err := Snapshot(newfs, "/")
+			if err != nil {
+				return false, err
+			}
+			err = Splice(fs, "/", snap)
+			if err != nil {
+				return false, err
+			}
+			fs.savedPDH.Store(coll.PortableDataHash)
+			return true, nil
+		}
+		fs.updateSignatures(coll.ManifestText)
+		return false, nil
+	}
+	if pdh := fs.savedPDH.Load().(string); pdh != "" {
+		var coll Collection
+		err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+pdh, nil, getparams)
+		if err != nil {
+			return false, err
+		}
+		fs.updateSignatures(coll.ManifestText)
+	}
+	return false, 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(false)
+		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 {
-	if fs.uuid == "" {
+	refreshed, err := fs.checkChangesOnServer(true)
+	if err != nil {
+		return err
+	}
+	if refreshed || fs.uuid == "" {
 		return nil
 	}
 	txt, err := fs.MarshalManifest(".")
 	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)
+		return fmt.Errorf("sync failed: update %s: %w", fs.uuid, err)
 	}
+	fs.updateSignatures(coll.ManifestText)
+	fs.savedPDH.Store(coll.PortableDataHash)
 	return nil
 }
 
@@ -237,8 +469,6 @@ func (fs *collectionFileSystem) Flush(path string, shortBlocks bool) error {
 }
 
 func (fs *collectionFileSystem) MemorySize() int64 {
-	fs.fileSystem.root.Lock()
-	defer fs.fileSystem.root.Unlock()
 	return fs.fileSystem.root.(*dirnode).MemorySize()
 }
 
@@ -252,6 +482,14 @@ 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
@@ -275,9 +513,9 @@ type filenodePtr struct {
 //
 // After seeking:
 //
-//     ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
-//     ||
-//     filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
+//	ptr.segmentIdx == len(filenode.segments) // i.e., at EOF
+//	||
+//	filenode.segments[ptr.segmentIdx].Len() > ptr.segmentOff
 func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
 	ptr = startPtr
 	if ptr.off < 0 {
@@ -362,6 +600,16 @@ func (fn *filenode) FS() FileSystem {
 	return fn.fs
 }
 
+func (fn *filenode) MemorySize() (size int64) {
+	fn.RLock()
+	defer fn.RUnlock()
+	size = 64
+	for _, seg := range fn.segments {
+		size += seg.memorySize()
+	}
+	return
+}
+
 // Read reads file data from a single segment, starting at startPtr,
 // into p. startPtr is assumed not to be up-to-date. Caller must have
 // RLock or Lock.
@@ -375,6 +623,10 @@ 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)
@@ -667,6 +919,47 @@ 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
@@ -891,23 +1184,16 @@ func (dn *dirnode) flush(ctx context.Context, names []string, opts flushOpts) er
 	return cg.Wait()
 }
 
-// caller must have write lock.
 func (dn *dirnode) MemorySize() (size int64) {
-	for _, name := range dn.sortedNames() {
-		node := dn.inodes[name]
-		node.Lock()
-		defer node.Unlock()
-		switch node := node.(type) {
-		case *dirnode:
-			size += node.MemorySize()
-		case *filenode:
-			for _, seg := range node.segments {
-				switch seg := seg.(type) {
-				case *memSegment:
-					size += int64(seg.Len())
-				}
-			}
-		}
+	dn.RLock()
+	todo := make([]inode, 0, len(dn.inodes))
+	for _, node := range dn.inodes {
+		todo = append(todo, node)
+	}
+	dn.RUnlock()
+	size = 64
+	for _, node := range todo {
+		size += node.MemorySize()
 	}
 	return
 }
@@ -1280,12 +1566,93 @@ 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
 	// Return a new segment with a subsection of the data from this
 	// one. length<0 means length=Len()-off.
 	Slice(off int, length int) segment
+	memorySize() int64
 }
 
 type memSegment struct {
@@ -1364,6 +1731,10 @@ func (me *memSegment) ReadAt(p []byte, off int64) (n int, err error) {
 	return
 }
 
+func (me *memSegment) memorySize() int64 {
+	return 64 + int64(len(me.buf))
+}
+
 type storedSegment struct {
 	kc      fsBackend
 	locator string
@@ -1401,6 +1772,10 @@ func (se storedSegment) ReadAt(p []byte, off int64) (n int, err error) {
 	return se.kc.ReadAt(se.locator, p, int(off)+se.offset)
 }
 
+func (se storedSegment) memorySize() int64 {
+	return 64 + int64(len(se.locator))
+}
+
 func canonicalName(name string) string {
 	name = path.Clean("/" + name)
 	if name == "/" || name == "./" {