1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
18 "git.arvados.org/arvados.git/sdk/go/arvados"
19 "git.arvados.org/arvados.git/sdk/go/keepclient"
20 "git.arvados.org/arvados.git/sdk/go/manifest"
21 "github.com/bmatcuk/doublestar/v4"
24 type printfer interface {
25 Printf(string, ...interface{})
28 var errTooManySymlinks = errors.New("too many symlinks, or symlink cycle")
30 const limitFollowSymlinks = 10
32 type filetodo struct {
38 // copier copies data from a finished container's output path to a new
39 // Arvados collection.
41 // Regular files (and symlinks to regular files) in hostOutputDir are
42 // copied from the local filesystem.
44 // Symlinks to mounted collections, and any collections mounted under
45 // ctrOutputDir, are copied by transforming the relevant parts of the
46 // existing manifests, without moving any data around.
48 // Symlinks to other parts of the container's filesystem result in
53 // manifest, err := (&copier{...}).Copy()
55 client *arvados.Client
56 keepClient IKeepClient
60 bindmounts map[string]bindmount
61 mounts map[string]arvados.Mount
62 secretMounts map[string]arvados.Mount
69 manifestCache map[string]*manifest.Manifest
72 // Copy copies data as needed, and returns a new manifest.
73 func (cp *copier) Copy() (string, error) {
74 err := cp.walkMount("", cp.ctrOutputDir, limitFollowSymlinks, true)
76 return "", fmt.Errorf("error scanning files to copy to output: %v", err)
78 collfs, err := (&arvados.Collection{ManifestText: cp.manifest}).FileSystem(cp.client, cp.keepClient)
80 return "", fmt.Errorf("error creating Collection.FileSystem: %v", err)
83 // Remove files/dirs that don't match globs (the ones that
84 // were added during cp.walkMount() by copying subtree
85 // manifests into cp.manifest).
86 err = cp.applyGlobsToCollectionFS(collfs)
88 return "", fmt.Errorf("error while removing non-matching files from output collection: %w", err)
90 // Remove files/dirs that don't match globs (the ones that are
91 // stored on the local filesystem and would need to be copied
92 // in copyFile() below).
93 cp.applyGlobsToFilesAndDirs()
94 for _, d := range cp.dirs {
95 err = collfs.Mkdir(d, 0777)
96 if err != nil && err != os.ErrExist {
97 return "", fmt.Errorf("error making directory %q in output collection: %v", d, err)
102 var lastparentdir string
103 for _, f := range cp.files {
104 // If a dir has just had its last file added, do a
105 // full Flush. Otherwise, do a partial Flush (write
106 // full-size blocks, but leave the last short block
107 // open so f's data can be packed with it).
108 dir, _ := filepath.Split(f.dst)
109 if dir != lastparentdir || unflushed > keepclient.BLOCKSIZE {
110 if err := collfs.Flush("/"+lastparentdir, dir != lastparentdir); err != nil {
111 return "", fmt.Errorf("error flushing output collection file data: %v", err)
117 n, err := cp.copyFile(collfs, f)
119 return "", fmt.Errorf("error copying file %q into output collection: %v", f, err)
123 return collfs.MarshalManifest(".")
126 func (cp *copier) matchGlobs(path string, isDir bool) bool {
127 // An entry in the top level of the output directory looks
128 // like "/foo", but globs look like "foo", so we strip the
129 // leading "/" before matching.
130 path = strings.TrimLeft(path, "/")
131 for _, glob := range cp.globs {
132 if !isDir && strings.HasSuffix(glob, "/**") {
133 // doublestar.Match("f*/**", "ff") and
134 // doublestar.Match("f*/**", "ff/gg") both
135 // return true, but (to be compatible with
136 // bash shopt) "ff" should match only if it is
139 // To avoid errant matches, we add the file's
140 // basename to the end of the pattern:
142 // Match("f*/**/ff", "ff") => false
143 // Match("f*/**/gg", "ff/gg") => true
145 // Of course, we need to escape basename in
146 // case it contains *, ?, \, etc.
147 _, name := filepath.Split(path)
148 escapedName := strings.TrimSuffix(strings.Replace(name, "", "\\", -1), "\\")
149 if match, _ := doublestar.Match(glob+"/"+escapedName, path); match {
152 } else if match, _ := doublestar.Match(glob, path); match {
155 // Workaround doublestar bug (v4.6.1).
156 // "foo*/**" should match "foo", but does not,
157 // because isZeroLengthPattern does not accept
158 // "*/**" as a zero length pattern.
159 if trunc := strings.TrimSuffix(glob, "*/**"); trunc != glob {
160 if match, _ := doublestar.Match(trunc, path); match {
169 // Delete entries from cp.files that do not match cp.globs.
171 // Delete entries from cp.dirs that do not match cp.globs.
173 // Ensure parent/ancestor directories of remaining cp.files and
174 // cp.dirs entries are still present in cp.dirs, even if they do not
175 // match cp.globs themselves.
176 func (cp *copier) applyGlobsToFilesAndDirs() {
177 if len(cp.globs) == 0 {
180 keepdirs := make(map[string]bool)
181 for _, path := range cp.dirs {
182 if cp.matchGlobs(path, true) {
183 keepdirs[path] = true
186 for path := range keepdirs {
187 for i, c := range path {
188 if i > 0 && c == '/' {
189 keepdirs[path[:i]] = true
193 var keepfiles []filetodo
194 for _, file := range cp.files {
195 if cp.matchGlobs(file.dst, false) {
196 keepfiles = append(keepfiles, file)
199 for _, file := range keepfiles {
200 for i, c := range file.dst {
201 if i > 0 && c == '/' {
202 keepdirs[file.dst[:i]] = true
207 for path := range keepdirs {
208 cp.dirs = append(cp.dirs, path)
210 sort.Strings(cp.dirs)
214 // Delete files in collfs that do not match cp.globs. Also delete
215 // directories that are empty (after deleting non-matching files) and
216 // do not match cp.globs themselves.
217 func (cp *copier) applyGlobsToCollectionFS(collfs arvados.CollectionFileSystem) error {
218 if len(cp.globs) == 0 {
221 include := make(map[string]bool)
222 err := fs.WalkDir(arvados.FS(collfs), "", func(path string, ent fs.DirEntry, err error) error {
223 if cp.matchGlobs(path, ent.IsDir()) {
224 for i, c := range path {
225 if i > 0 && c == '/' {
226 include[path[:i]] = true
236 err = fs.WalkDir(arvados.FS(collfs), "", func(path string, ent fs.DirEntry, err error) error {
237 if err != nil || path == "" {
241 err := collfs.RemoveAll(path)
254 // Return true if it's possible for any descendant of the given path
255 // to match anything in cp.globs. Used by walkMount to avoid loading
256 // collections that are mounted underneath ctrOutputPath but excluded
258 func (cp *copier) subtreeCouldMatch(path string) bool {
259 if len(cp.globs) == 0 {
262 pathdepth := 1 + strings.Count(path, "/")
263 for _, glob := range cp.globs {
266 for i, c := range glob {
267 if c != '/' || !doublestar.ValidatePattern(glob[:i]) {
268 // Escaped "/", or "/" in a character
269 // class, is not a path separator.
272 if glob[lastsep:i] == "**" {
276 if globdepth++; globdepth == pathdepth {
277 if match, _ := doublestar.Match(glob[:i]+"/*", path+"/z"); match {
283 if globdepth < pathdepth && glob[lastsep:] == "**" {
290 func (cp *copier) copyFile(fs arvados.CollectionFileSystem, f filetodo) (int64, error) {
291 cp.logger.Printf("copying %q (%d bytes)", strings.TrimLeft(f.dst, "/"), f.size)
292 dst, err := fs.OpenFile(f.dst, os.O_CREATE|os.O_WRONLY, 0666)
296 src, err := os.Open(f.src)
302 n, err := io.Copy(dst, src)
307 return n, dst.Close()
310 // Append to cp.manifest, cp.files, and cp.dirs so as to copy src (an
311 // absolute path in the container's filesystem) to dest (an absolute
312 // path in the output collection, or "" for output root).
314 // src must be (or be a descendant of) a readonly "collection" mount,
315 // a writable collection mounted at ctrOutputPath, or a "tmp" mount.
317 // If walkMountsBelow is true, include contents of any collection
318 // mounted below src as well.
319 func (cp *copier) walkMount(dest, src string, maxSymlinks int, walkMountsBelow bool) error {
320 // srcRoot, srcMount indicate the innermost mount that
323 var srcMount arvados.Mount
324 for root, mnt := range cp.mounts {
325 if len(root) > len(srcRoot) && strings.HasPrefix(src+"/", root+"/") {
326 srcRoot, srcMount = root, mnt
329 for root := range cp.secretMounts {
330 if len(root) > len(srcRoot) && strings.HasPrefix(src+"/", root+"/") {
331 // Silently omit secrets, and symlinks to
337 return fmt.Errorf("cannot output file %q: not in any mount", src)
340 // srcRelPath is the path to the file/dir we are trying to
341 // copy, relative to its mount point -- ".", "./foo.txt", ...
342 srcRelPath := filepath.Join(".", srcMount.Path, src[len(srcRoot):])
344 // outputRelPath is the destination path relative to the
345 // output directory. Used for logging and glob matching.
346 var outputRelPath = ""
347 if strings.HasPrefix(src, cp.ctrOutputDir) {
348 outputRelPath = strings.TrimPrefix(src[len(cp.ctrOutputDir):], "/")
350 if outputRelPath == "" {
351 // blank means copy a whole directory, so replace it
352 // with a wildcard to make it a little clearer what's
353 // going on since outputRelPath is only used for logging
358 case srcMount.ExcludeFromOutput:
359 case outputRelPath != "*" && !cp.subtreeCouldMatch(outputRelPath):
360 cp.logger.Printf("not copying %q because contents cannot match output globs", outputRelPath)
362 case srcMount.Kind == "tmp":
363 // Handle by walking the host filesystem.
364 return cp.walkHostFS(dest, src, maxSymlinks, walkMountsBelow)
365 case srcMount.Kind != "collection":
366 return fmt.Errorf("%q: unsupported mount %q in output (kind is %q)", src, srcRoot, srcMount.Kind)
367 case !srcMount.Writable:
368 cp.logger.Printf("copying %q from %v/%v", outputRelPath, srcMount.PortableDataHash, strings.TrimPrefix(srcRelPath, "./"))
369 mft, err := cp.getManifest(srcMount.PortableDataHash)
373 cp.manifest += mft.Extract(srcRelPath, dest).Text
375 cp.logger.Printf("copying %q", outputRelPath)
376 hostRoot, err := cp.hostRoot(srcRoot)
380 f, err := os.Open(filepath.Join(hostRoot, ".arvados#collection"))
385 var coll arvados.Collection
386 err = json.NewDecoder(f).Decode(&coll)
390 mft := manifest.Manifest{Text: coll.ManifestText}
391 cp.manifest += mft.Extract(srcRelPath, dest).Text
394 return cp.walkMountsBelow(dest, src)
399 func (cp *copier) walkMountsBelow(dest, src string) error {
400 for mnt, mntinfo := range cp.mounts {
401 if !strings.HasPrefix(mnt, src+"/") {
404 if cp.copyRegularFiles(mntinfo) {
405 // These got copied into the nearest parent
406 // mount as regular files during setup, so
407 // they get copied as regular files when we
408 // process the parent. Output will reflect any
409 // changes and deletions done by the
413 // Example: we are processing dest=/foo src=/mnt1/dir1
414 // (perhaps we followed a symlink /outdir/foo ->
415 // /mnt1/dir1). Caller has already processed the
416 // collection mounted at /mnt1, but now we find that
417 // /mnt1/dir1/mnt2 is also a mount, so we need to copy
418 // src=/mnt1/dir1/mnt2 to dest=/foo/mnt2.
420 // We handle all descendants of /mnt1/dir1 in this
421 // loop instead of using recursion:
422 // /mnt1/dir1/mnt2/mnt3 is a child of both /mnt1 and
423 // /mnt1/dir1/mnt2, but we only want to walk it
424 // once. (This simplification is safe because mounted
425 // collections cannot contain symlinks.)
426 err := cp.walkMount(dest+mnt[len(src):], mnt, 0, false)
434 // Add entries to cp.dirs and cp.files so as to copy src (an absolute
435 // path in the container's filesystem which corresponds to a real file
436 // or directory in cp.hostOutputDir) to dest (an absolute path in the
437 // output collection, or "" for output root).
439 // Always follow symlinks.
441 // If includeMounts is true, include mounts at and below src.
442 // Otherwise, skip them.
443 func (cp *copier) walkHostFS(dest, src string, maxSymlinks int, includeMounts bool) error {
445 err := cp.walkMountsBelow(dest, src)
451 hostsrc := cp.hostOutputDir + src[len(cp.ctrOutputDir):]
453 // If src is a symlink, walk its target.
454 fi, err := os.Lstat(hostsrc)
456 return fmt.Errorf("lstat %q: %s", src, err)
458 if fi.Mode()&os.ModeSymlink != 0 {
460 return errTooManySymlinks
462 target, err := os.Readlink(hostsrc)
464 return fmt.Errorf("readlink %q: %s", src, err)
466 if !strings.HasPrefix(target, "/") {
467 target = filepath.Join(filepath.Dir(src), target)
469 return cp.walkMount(dest, target, maxSymlinks-1, true)
472 // If src is a regular directory, append it to cp.dirs and
473 // walk each of its children. (If there are no children,
474 // create an empty file "dest/.keep".)
475 if fi.Mode().IsDir() {
477 cp.dirs = append(cp.dirs, dest)
479 dir, err := os.Open(hostsrc)
481 return fmt.Errorf("open %q: %s", src, err)
483 names, err := dir.Readdirnames(-1)
486 return fmt.Errorf("readdirnames %q: %s", src, err)
490 cp.files = append(cp.files, filetodo{
492 dst: dest + "/.keep",
498 for _, name := range names {
499 dest, src := dest+"/"+name, src+"/"+name
500 if _, isSecret := cp.secretMounts[src]; isSecret {
503 if mntinfo, isMount := cp.mounts[src]; isMount && !cp.copyRegularFiles(mntinfo) {
504 // If a regular file/dir somehow
505 // exists at a path that's also a
506 // mount target, ignore the file --
507 // the mount has already been included
508 // with walkMountsBelow().
510 // (...except mount types that are
511 // handled as regular files.)
513 } else if isMount && !cp.subtreeCouldMatch(src[len(cp.ctrOutputDir)+1:]) {
516 err = cp.walkHostFS(dest, src, maxSymlinks, false)
524 // If src is a regular file, append it to cp.files.
525 if fi.Mode().IsRegular() {
526 cp.files = append(cp.files, filetodo{
533 cp.logger.Printf("Skipping unsupported file type (mode %o) in output dir: %q", fi.Mode(), src)
537 // Return the host path that was mounted at the given path in the
539 func (cp *copier) hostRoot(ctrRoot string) (string, error) {
540 if ctrRoot == cp.ctrOutputDir {
541 return cp.hostOutputDir, nil
543 if mnt, ok := cp.bindmounts[ctrRoot]; ok {
544 return mnt.HostPath, nil
546 return "", fmt.Errorf("not bind-mounted: %q", ctrRoot)
549 func (cp *copier) copyRegularFiles(m arvados.Mount) bool {
550 return m.Kind == "text" || m.Kind == "json" || (m.Kind == "collection" && m.Writable)
553 func (cp *copier) getManifest(pdh string) (*manifest.Manifest, error) {
554 if mft, ok := cp.manifestCache[pdh]; ok {
557 var coll arvados.Collection
558 err := cp.client.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+pdh, nil, nil)
560 return nil, fmt.Errorf("error retrieving collection record for %q: %s", pdh, err)
562 mft := &manifest.Manifest{Text: coll.ManifestText}
563 if cp.manifestCache == nil {
564 cp.manifestCache = map[string]*manifest.Manifest{pdh: mft}
566 cp.manifestCache[pdh] = mft