[ARVADOS] created: 1.1.0-134-gda3f228
Git user
git at public.curoverse.com
Fri Nov 10 16:34:50 EST 2017
at da3f22835804cc1bafe7daf373867ef46cbb20e8 (commit)
commit da3f22835804cc1bafe7daf373867ef46cbb20e8
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Fri Nov 10 16:34:28 2017 -0500
12483: Add basic file writing tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/sdk/go/arvados/collection_fs_test.go b/sdk/go/arvados/collection_fs_test.go
index 7bd3570..605c41c 100644
--- a/sdk/go/arvados/collection_fs_test.go
+++ b/sdk/go/arvados/collection_fs_test.go
@@ -135,14 +135,80 @@ func (s *CollectionFSSuite) TestNotExist(c *check.C) {
}
}
-func (s *CollectionFSSuite) TestOpenFile(c *check.C) {
- c.Skip("cannot test files with nil keepclient")
+func (s *CollectionFSSuite) TestReadOnlyFile(c *check.C) {
+ f, err := s.fs.OpenFile("/dir1/foo", os.O_RDONLY, 0)
+ c.Assert(err, check.IsNil)
+ st, err := f.Stat()
+ c.Assert(err, check.IsNil)
+ c.Check(st.Size(), check.Equals, int64(3))
+ n, err := f.Write([]byte("bar"))
+ c.Check(n, check.Equals, 0)
+ c.Check(err, check.Equals, ErrReadOnlyFile)
+}
+
+func (s *CollectionFSSuite) TestCreateFile(c *check.C) {
+ f, err := s.fs.OpenFile("/newfile", os.O_RDWR|os.O_CREATE, 0)
+ c.Assert(err, check.IsNil)
+ st, err := f.Stat()
+ c.Assert(err, check.IsNil)
+ c.Check(st.Size(), check.Equals, int64(0))
+
+ n, err := f.Write([]byte("bar"))
+ c.Check(n, check.Equals, 3)
+ c.Check(err, check.IsNil)
+
+ c.Check(f.Close(), check.IsNil)
+
+ f, err = s.fs.OpenFile("/newfile", os.O_RDWR|os.O_CREATE|os.O_EXCL, 0)
+ c.Check(f, check.IsNil)
+ c.Assert(err, check.NotNil)
+
+ f, err = s.fs.OpenFile("/newfile", os.O_RDWR, 0)
+ c.Assert(err, check.IsNil)
+ st, err = f.Stat()
+ c.Assert(err, check.IsNil)
+ c.Check(st.Size(), check.Equals, int64(3))
+
+ c.Check(f.Close(), check.IsNil)
+
+ // TODO: serialize to Collection, confirm manifest contents,
+ // make new FileSystem, confirm file contents.
+}
- f, err := s.fs.Open("/foo.txt")
+func (s *CollectionFSSuite) TestReadWriteFile(c *check.C) {
+ f, err := s.fs.OpenFile("/dir1/foo", os.O_RDWR, 0)
c.Assert(err, check.IsNil)
st, err := f.Stat()
c.Assert(err, check.IsNil)
c.Check(st.Size(), check.Equals, int64(3))
+
+ buf := make([]byte, 4)
+ n, err := f.Read(buf)
+ c.Check(n, check.Equals, 3)
+ c.Check(err, check.Equals, io.EOF)
+ c.Check(string(buf[:3]), check.DeepEquals, "foo")
+
+ pos, err := f.Seek(-2, os.SEEK_CUR)
+ c.Check(pos, check.Equals, int64(1))
+ c.Check(err, check.IsNil)
+
+ n, err = f.Write([]byte("*"))
+ c.Check(n, check.Equals, 1)
+ c.Check(err, check.IsNil)
+
+ pos, err = f.Seek(0, os.SEEK_CUR)
+ c.Check(pos, check.Equals, int64(2))
+ c.Check(err, check.IsNil)
+
+ pos, err = f.Seek(0, os.SEEK_SET)
+ c.Check(pos, check.Equals, int64(0))
+ c.Check(err, check.IsNil)
+
+ buf = make([]byte, 4)
+ n, err = f.Read(buf)
+ c.Check(n, check.Equals, 3)
+ c.Check(err, check.Equals, io.EOF)
+ c.Check(string(buf[:3]), check.Equals, "f*o")
}
// Gocheck boilerplate
commit 3e3abb01d17b0968e22e6738da12c86ad0a2a06c
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Thu Nov 9 13:24:34 2017 -0500
12483: Rewrite collection filesystem.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/sdk/go/arvados/collection_fs.go b/sdk/go/arvados/collection_fs.go
index 1acf274..1dee6f1 100644
--- a/sdk/go/arvados/collection_fs.go
+++ b/sdk/go/arvados/collection_fs.go
@@ -5,268 +5,647 @@
package arvados
import (
+ "errors"
"io"
"net/http"
"os"
"path"
+ "regexp"
+ "strconv"
"strings"
"sync"
"time"
+)
- "git.curoverse.com/arvados.git/sdk/go/manifest"
+var (
+ ErrReadOnlyFile = errors.New("read-only file")
+ ErrNegativeOffset = errors.New("cannot seek to negative offset")
+ ErrFileExists = errors.New("file exists")
+ ErrInvalidOperation = errors.New("invalid operation")
+ ErrPermission = os.ErrPermission
)
type File interface {
io.Reader
+ io.Writer
io.Closer
io.Seeker
Size() int64
+ Readdir(int) ([]os.FileInfo, error)
+ Stat() (os.FileInfo, error)
}
type keepClient interface {
- ManifestFileReader(manifest.Manifest, string) (File, error)
+ ReadAt(locator string, p []byte, off int64) (int, error)
}
-type collectionFile struct {
- File
- collection *Collection
- name string
- size int64
+type fileinfo struct {
+ name string
+ mode os.FileMode
+ size int64
+ modTime time.Time
}
-func (cf *collectionFile) Size() int64 {
- return cf.size
+// Name implements os.FileInfo.
+func (fi fileinfo) Name() string {
+ return fi.name
}
-func (cf *collectionFile) Readdir(count int) ([]os.FileInfo, error) {
- return nil, io.EOF
+// ModTime implements os.FileInfo.
+func (fi fileinfo) ModTime() time.Time {
+ return fi.modTime
}
-func (cf *collectionFile) Stat() (os.FileInfo, error) {
- return collectionDirent{
- collection: cf.collection,
- name: cf.name,
- size: cf.size,
- isDir: false,
- }, nil
+// Mode implements os.FileInfo.
+func (fi fileinfo) Mode() os.FileMode {
+ return fi.mode
}
-type collectionDir struct {
- collection *Collection
- stream string
- dirents []os.FileInfo
+// IsDir implements os.FileInfo.
+func (fi fileinfo) IsDir() bool {
+ return fi.mode&os.ModeDir != 0
}
-// Readdir implements os.File.
-func (cd *collectionDir) Readdir(count int) ([]os.FileInfo, error) {
- ret := cd.dirents
- if count <= 0 {
- cd.dirents = nil
- return ret, nil
- } else if len(ret) == 0 {
- return nil, io.EOF
- }
- var err error
- if count >= len(ret) {
- count = len(ret)
- err = io.EOF
- }
- cd.dirents = cd.dirents[count:]
- return ret[:count], err
+// Size implements os.FileInfo.
+func (fi fileinfo) Size() int64 {
+ return fi.size
}
-// Stat implements os.File.
-func (cd *collectionDir) Stat() (os.FileInfo, error) {
- return collectionDirent{
- collection: cd.collection,
- name: path.Base(cd.stream),
- isDir: true,
- size: int64(len(cd.dirents)),
- }, nil
+// Sys implements os.FileInfo.
+func (fi fileinfo) Sys() interface{} {
+ return nil
}
-// Close implements os.File.
-func (cd *collectionDir) Close() error {
- return nil
+func (fi fileinfo) Stat() os.FileInfo {
+ return fi
}
-// Read implements os.File.
-func (cd *collectionDir) Read([]byte) (int, error) {
- return 0, nil
+// A CollectionFileSystem is an http.Filesystem plus Stat() and
+// support for opening writable files.
+type CollectionFileSystem interface {
+ http.FileSystem
+ Stat(name string) (os.FileInfo, error)
+ Create(name string) (File, error)
+ OpenFile(name string, flag int, perm os.FileMode) (File, error)
}
-// Seek implements os.File.
-func (cd *collectionDir) Seek(int64, int) (int64, error) {
- return 0, nil
+type fileSystem struct {
+ dirnode
}
-// collectionDirent implements os.FileInfo.
-type collectionDirent struct {
- collection *Collection
- name string
- isDir bool
- mode os.FileMode
- size int64
+func (fs *fileSystem) OpenFile(name string, flag int, perm os.FileMode) (File, error) {
+ return fs.dirnode.OpenFile(path.Clean(name), flag, perm)
}
-// Name implements os.FileInfo.
-func (e collectionDirent) Name() string {
- return e.name
+func (fs *fileSystem) Open(name string) (http.File, error) {
+ return fs.dirnode.OpenFile(path.Clean(name), os.O_RDONLY, 0)
}
-// ModTime implements os.FileInfo.
-func (e collectionDirent) ModTime() time.Time {
- if e.collection.ModifiedAt == nil {
- return time.Now()
+func (fs *fileSystem) Create(name string) (File, error) {
+ return fs.dirnode.OpenFile(path.Clean(name), os.O_CREATE|os.O_RDWR|os.O_TRUNC, 0)
+}
+
+func (fs *fileSystem) Stat(name string) (os.FileInfo, error) {
+ f, err := fs.OpenFile(name, os.O_RDONLY, 0)
+ if err != nil {
+ return nil, err
}
- return *e.collection.ModifiedAt
+ defer f.Close()
+ return f.Stat()
}
-// Mode implements os.FileInfo.
-func (e collectionDirent) Mode() os.FileMode {
- if e.isDir {
- return 0555
- } else {
- return 0444
+type inode interface {
+ os.FileInfo
+ OpenFile(string, int, os.FileMode) (*file, error)
+ Parent() inode
+ Read([]byte, filenodePtr) (int, filenodePtr, error)
+ Write([]byte, filenodePtr) (int, filenodePtr, error)
+ Readdir() []os.FileInfo
+ Stat() os.FileInfo
+ sync.Locker
+ RLock()
+ RUnlock()
+}
+
+// filenode implements inode.
+type filenode struct {
+ fileinfo
+ parent *dirnode
+ extents []extent
+ repacked int64 // number of times anything in []extents has changed len
+ sync.RWMutex
+}
+
+// filenodePtr is an offset into a file that is (usually) efficient to
+// seek to. Specifically, if filenode.repacked==filenodePtr.repacked
+// then filenode.extents[filenodePtr.extentIdx][filenodePtr.extentOff]
+// corresponds to file offset filenodePtr.off. Otherwise, it is
+// necessary to reexamine len(filenode.extents[0]) etc. to find the
+// correct extent and offset.
+type filenodePtr struct {
+ off int64
+ extentIdx int
+ extentOff int
+ repacked int64
+}
+
+// seek returns a ptr that is consistent with both startPtr.off and
+// the current state of fn. The caller must already hold fn.RLock() or
+// fn.Lock().
+//
+// If startPtr points beyond the end of the file, ptr will point to
+// exactly the end of the file.
+//
+// After seeking:
+//
+// ptr.extentIdx == len(filenode.extents) // i.e., at EOF
+// ||
+// filenode.extents[ptr.extentIdx].Len() >= ptr.extentOff
+func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) {
+ ptr = startPtr
+ if ptr.off < 0 {
+ // meaningless anyway
+ return
+ } else if ptr.off >= fn.fileinfo.size {
+ ptr.off = fn.fileinfo.size
+ ptr.extentIdx = len(fn.extents)
+ ptr.extentOff = 0
+ ptr.repacked = fn.repacked
+ return
+ } else if ptr.repacked == fn.repacked {
+ // extentIdx and extentOff accurately reflect ptr.off,
+ // but might have fallen off the end of an extent
+ if int64(ptr.extentOff) >= fn.extents[ptr.extentIdx].Len() {
+ ptr.extentIdx++
+ ptr.extentOff = 0
+ }
+ return
+ }
+ defer func() {
+ ptr.repacked = fn.repacked
+ }()
+ if ptr.off >= fn.fileinfo.size {
+ ptr.extentIdx, ptr.extentOff = len(fn.extents), 0
+ return
}
+ // Recompute extentIdx and extentOff. We have already
+ // established fn.fileinfo.size > ptr.off >= 0, so we don't
+ // have to deal with edge cases here.
+ var off int64
+ for ptr.extentIdx, ptr.extentOff = 0, 0; off < ptr.off; ptr.extentIdx++ {
+ // This would panic (index out of range) if
+ // fn.fileinfo.size were larger than
+ // sum(fn.extents[i].Len()) -- but that can't happen
+ // because we have ensured fn.fileinfo.size is always
+ // accurate.
+ extLen := fn.extents[ptr.extentIdx].Len()
+ if off+extLen > ptr.off {
+ ptr.extentOff = int(ptr.off - off)
+ break
+ }
+ off += extLen
+ }
+ return
}
-// IsDir implements os.FileInfo.
-func (e collectionDirent) IsDir() bool {
- return e.isDir
+func (fn *filenode) appendExtent(e extent) {
+ fn.Lock()
+ defer fn.Unlock()
+ fn.extents = append(fn.extents, e)
+ fn.fileinfo.size += e.Len()
+ fn.repacked++
}
-// Size implements os.FileInfo.
-func (e collectionDirent) Size() int64 {
- return e.size
+func (fn *filenode) OpenFile(string, int, os.FileMode) (*file, error) {
+ return nil, os.ErrNotExist
}
-// Sys implements os.FileInfo.
-func (e collectionDirent) Sys() interface{} {
+func (fn *filenode) Parent() inode {
+ return fn.parent
+}
+
+func (fn *filenode) Readdir() []os.FileInfo {
return nil
}
-// A CollectionFileSystem is an http.Filesystem with an added Stat() method.
-type CollectionFileSystem interface {
- http.FileSystem
- Stat(name string) (os.FileInfo, error)
+func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
+ fn.RLock()
+ defer fn.RUnlock()
+ ptr = fn.seek(startPtr)
+ if ptr.off < 0 {
+ err = ErrNegativeOffset
+ return
+ }
+ if ptr.extentIdx >= len(fn.extents) {
+ err = io.EOF
+ return
+ }
+ n, err = fn.extents[ptr.extentIdx].ReadAt(p, int64(ptr.extentOff))
+ if n > 0 {
+ ptr.off += int64(n)
+ ptr.extentOff += n
+ if int64(ptr.extentOff) == fn.extents[ptr.extentIdx].Len() {
+ ptr.extentIdx++
+ ptr.extentOff = 0
+ if ptr.extentIdx < len(fn.extents) && err == io.EOF {
+ err = nil
+ }
+ }
+ }
+ return
}
-// collectionFS implements CollectionFileSystem.
-type collectionFS struct {
- collection *Collection
- client *Client
- kc keepClient
- sizes map[string]int64
- sizesOnce sync.Once
+func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr, err error) {
+ fn.Lock()
+ defer fn.Unlock()
+ ptr = fn.seek(startPtr)
+ if ptr.off < 0 {
+ err = ErrNegativeOffset
+ return
+ }
+ err = ErrReadOnlyFile
+ return
}
// FileSystem returns a CollectionFileSystem for the collection.
func (c *Collection) FileSystem(client *Client, kc keepClient) CollectionFileSystem {
- return &collectionFS{
- collection: c,
- client: client,
- kc: kc,
- }
-}
-
-func (c *collectionFS) Stat(name string) (os.FileInfo, error) {
- name = canonicalName(name)
- if name == "." {
- return collectionDirent{
- collection: c.collection,
- name: "/",
- isDir: true,
- }, nil
- }
- if size, ok := c.fileSizes()[name]; ok {
- return collectionDirent{
- collection: c.collection,
- name: path.Base(name),
- size: size,
- isDir: false,
- }, nil
- }
- for fnm := range c.fileSizes() {
- if !strings.HasPrefix(fnm, name+"/") {
- continue
+ fs := &fileSystem{dirnode: dirnode{
+ cache: &keepBlockCache{kc: kc},
+ client: client,
+ kc: kc,
+ fileinfo: fileinfo{name: ".", mode: os.ModeDir | 0755},
+ parent: nil,
+ inodes: make(map[string]inode),
+ }}
+ fs.dirnode.parent = &fs.dirnode
+ fs.dirnode.loadManifest(c.ManifestText)
+ return fs
+}
+
+type file struct {
+ inode
+ ptr filenodePtr
+ append bool
+ writable bool
+ unreaddirs []os.FileInfo
+}
+
+func (f *file) Read(p []byte) (n int, err error) {
+ n, f.ptr, err = f.inode.Read(p, f.ptr)
+ return
+}
+
+func (f *file) Seek(off int64, whence int) (pos int64, err error) {
+ size := f.inode.Size()
+ ptr := f.ptr
+ switch whence {
+ case os.SEEK_SET:
+ ptr.off = off
+ case os.SEEK_CUR:
+ ptr.off += off
+ case os.SEEK_END:
+ ptr.off = size + off
+ }
+ if ptr.off < 0 {
+ return f.ptr.off, ErrNegativeOffset
+ }
+ if ptr.off > size {
+ ptr.off = size
+ }
+ if ptr.off != f.ptr.off {
+ f.ptr = ptr
+ // force filenode to recompute f.ptr fields on next
+ // use
+ f.ptr.repacked = -1
+ }
+ return f.ptr.off, nil
+}
+
+func (f *file) Write(p []byte) (n int, err error) {
+ n, f.ptr, err = f.inode.Write(p, f.ptr)
+ return
+}
+
+func (f *file) Readdir(count int) ([]os.FileInfo, error) {
+ if !f.inode.IsDir() {
+ return nil, ErrInvalidOperation
+ }
+ if count <= 0 {
+ return f.inode.Readdir(), nil
+ }
+ if f.unreaddirs == nil {
+ f.unreaddirs = f.inode.Readdir()
+ }
+ if len(f.unreaddirs) == 0 {
+ return nil, io.EOF
+ }
+ if count > len(f.unreaddirs) {
+ count = len(f.unreaddirs)
+ }
+ ret := f.unreaddirs[:count]
+ f.unreaddirs = f.unreaddirs[count:]
+ return ret, nil
+}
+
+func (f *file) Stat() (os.FileInfo, error) {
+ return f.inode, nil
+}
+
+func (f *file) Close() error {
+ // FIXME: flush
+ return nil
+}
+
+func (f *file) OpenFile(name string, flag int, perm os.FileMode) (*file, error) {
+ return f.inode.OpenFile(name, flag, perm)
+}
+
+type dirnode struct {
+ fileinfo
+ parent *dirnode
+ client *Client
+ kc keepClient
+ cache blockCache
+ inodes map[string]inode
+ sync.RWMutex
+}
+
+func (dn *dirnode) loadManifest(txt string) {
+ // FIXME: faster
+ var dirname string
+ for _, stream := range strings.Split(txt, "\n") {
+ var extents []storedExtent
+ for i, token := range strings.Split(stream, " ") {
+ if i == 0 {
+ dirname = manifestUnescape(token)
+ continue
+ }
+ if !strings.Contains(token, ":") {
+ toks := strings.SplitN(token, "+", 3)
+ if len(toks) < 2 {
+ // FIXME: broken
+ continue
+ }
+ length, err := strconv.ParseInt(toks[1], 10, 32)
+ if err != nil || length < 0 {
+ // FIXME: broken
+ continue
+ }
+ extents = append(extents, storedExtent{
+ locator: token,
+ offset: 0,
+ length: int(length),
+ })
+ continue
+ }
+ toks := strings.Split(token, ":")
+ if len(toks) != 3 {
+ // FIXME: broken manifest
+ continue
+ }
+ offset, err := strconv.ParseInt(toks[0], 10, 64)
+ if err != nil || offset < 0 {
+ // FIXME: broken manifest
+ continue
+ }
+ length, err := strconv.ParseInt(toks[1], 10, 64)
+ if err != nil || length < 0 {
+ // FIXME: broken manifest
+ continue
+ }
+ name := path.Clean(dirname + "/" + manifestUnescape(toks[2]))
+ dn.makeParentDirs(name)
+ f, err := dn.OpenFile(name, os.O_CREATE|os.O_WRONLY|os.O_APPEND, 0700)
+ if err != nil {
+ // FIXME: broken
+ continue
+ }
+ if f.inode.Stat().IsDir() {
+ f.Close()
+ // FIXME: broken manifest
+ continue
+ }
+ var pos int64
+ for _, e := range extents {
+ if pos+e.Len() < offset {
+ pos += e.Len()
+ continue
+ }
+ if pos > offset+length {
+ break
+ }
+ var blkOff int
+ if pos < offset {
+ blkOff = int(offset - pos)
+ }
+ blkLen := int(e.Len()) - blkOff
+ if pos+int64(blkOff+blkLen) > offset+length {
+ blkLen = int(offset + length - pos - int64(blkOff))
+ }
+ f.inode.(*filenode).appendExtent(storedExtent{
+ cache: dn.cache,
+ locator: e.locator,
+ offset: blkOff,
+ length: blkLen,
+ })
+ pos += e.Len()
+ }
+ f.Close()
}
- return collectionDirent{
- collection: c.collection,
- name: path.Base(name),
- isDir: true,
- }, nil
}
- return nil, os.ErrNotExist
}
-func (c *collectionFS) Open(name string) (http.File, error) {
- // Ensure name looks the way it does in a manifest.
- name = canonicalName(name)
+func (dn *dirnode) makeParentDirs(name string) {
+ names := strings.Split(name, "/")
+ for _, name := range names[:len(names)-1] {
+ dn.Lock()
+ defer dn.Unlock()
+ if n, ok := dn.inodes[name]; !ok {
+ n := &dirnode{
+ parent: dn,
+ client: dn.client,
+ kc: dn.kc,
+ fileinfo: fileinfo{
+ name: name,
+ mode: os.ModeDir | 0755,
+ },
+ }
+ if dn.inodes == nil {
+ dn.inodes = make(map[string]inode)
+ }
+ dn.inodes[name] = n
+ dn.fileinfo.size++
+ dn = n
+ } else if n, ok := n.(*dirnode); ok {
+ dn = n
+ } else {
+ // fail
+ return
+ }
+ }
+}
+
+func (dn *dirnode) Parent() inode {
+ return dn.parent
+}
+
+func (dn *dirnode) Readdir() (fi []os.FileInfo) {
+ dn.RLock()
+ defer dn.RUnlock()
+ fi = make([]os.FileInfo, 0, len(dn.inodes))
+ for _, inode := range dn.inodes {
+ fi = append(fi, inode.Stat())
+ }
+ return
+}
- m := manifest.Manifest{Text: c.collection.ManifestText}
+func (dn *dirnode) Read(p []byte, ptr filenodePtr) (int, filenodePtr, error) {
+ return 0, ptr, ErrInvalidOperation
+}
+
+func (dn *dirnode) Write(p []byte, ptr filenodePtr) (int, filenodePtr, error) {
+ return 0, ptr, ErrInvalidOperation
+}
- // Return a file if it exists.
- if size, ok := c.fileSizes()[name]; ok {
- reader, err := c.kc.ManifestFileReader(m, name)
+func (dn *dirnode) OpenFile(name string, flag int, perm os.FileMode) (*file, error) {
+ name = strings.TrimSuffix(name, "/")
+ if name == "." || name == "" {
+ return &file{inode: dn}, nil
+ }
+ if dirname, name := path.Split(name); dirname != "" {
+ // OpenFile("foo/bar/baz") =>
+ // OpenFile("foo/bar").OpenFile("baz") (or
+ // ErrNotExist, if foo/bar is a file)
+ f, err := dn.OpenFile(dirname, os.O_RDONLY, 0)
if err != nil {
return nil, err
}
- return &collectionFile{
- File: reader,
- collection: c.collection,
- name: path.Base(name),
- size: size,
- }, nil
- }
-
- // Return a directory if it's the root dir or there are file
- // entries below it.
- children := map[string]collectionDirent{}
- for fnm, size := range c.fileSizes() {
- if !strings.HasPrefix(fnm, name+"/") {
- continue
+ defer f.Close()
+ if dn, ok := f.inode.(*dirnode); ok {
+ return dn.OpenFile(name, flag, perm)
+ } else {
+ return nil, os.ErrNotExist
+ }
+ }
+ dn.Lock()
+ defer dn.Unlock()
+ if name == ".." {
+ return &file{inode: dn.parent}, nil
+ }
+ n, ok := dn.inodes[name]
+ if !ok {
+ if flag&os.O_CREATE == 0 {
+ return nil, os.ErrNotExist
+ }
+ n = &filenode{
+ parent: dn,
+ fileinfo: fileinfo{
+ name: name,
+ mode: 0755,
+ },
}
- isDir := false
- ent := fnm[len(name)+1:]
- if i := strings.Index(ent, "/"); i >= 0 {
- ent = ent[:i]
- isDir = true
+ if dn.inodes == nil {
+ dn.inodes = make(map[string]inode)
}
- e := children[ent]
- e.collection = c.collection
- e.isDir = isDir
- e.name = ent
- e.size = size
- children[ent] = e
- }
- if len(children) == 0 && name != "." {
- return nil, os.ErrNotExist
- }
- dirents := make([]os.FileInfo, 0, len(children))
- for _, ent := range children {
- dirents = append(dirents, ent)
- }
- return &collectionDir{
- collection: c.collection,
- stream: name,
- dirents: dirents,
+ dn.inodes[name] = n
+ dn.fileinfo.size++
+ } else if flag&os.O_EXCL != 0 {
+ return nil, ErrFileExists
+ }
+ return &file{
+ inode: n,
+ append: flag&os.O_APPEND != 0,
+ writable: flag&(os.O_WRONLY|os.O_RDWR) != 0,
}, nil
}
-// fileSizes returns a map of files that can be opened. Each key
-// starts with "./".
-func (c *collectionFS) fileSizes() map[string]int64 {
- c.sizesOnce.Do(func() {
- c.sizes = map[string]int64{}
- m := manifest.Manifest{Text: c.collection.ManifestText}
- for ms := range m.StreamIter() {
- for _, fss := range ms.FileStreamSegments {
- c.sizes[ms.StreamName+"/"+fss.Name] += int64(fss.SegLen)
- }
+type extent interface {
+ io.ReaderAt
+ Len() int64
+}
+
+type writableExtent interface {
+ extent
+ WriteAt(p []byte, off int)
+ Truncate(n int)
+}
+
+type memExtent struct {
+ buf []byte
+}
+
+func (me *memExtent) Len() int64 {
+ return int64(len(me.buf))
+}
+
+func (me *memExtent) Truncate(n int) {
+ if n > cap(me.buf) {
+ newsize := 1024
+ for newsize < n {
+ newsize = newsize << 2
+ }
+ newbuf := make([]byte, n, newsize)
+ copy(newbuf, me.buf)
+ me.buf = newbuf
+ }
+ me.buf = me.buf[:n]
+}
+
+func (me *memExtent) WriteAt(p []byte, off int) {
+ if off+len(p) > len(me.buf) {
+ panic("overflowed extent")
+ }
+ copy(me.buf[off:], p)
+}
+
+func (me *memExtent) ReadAt(p []byte, off int64) (n int, err error) {
+ if off > me.Len() {
+ err = io.EOF
+ return
+ }
+ n = copy(p, me.buf[int(off):])
+ if n < len(p) {
+ err = io.EOF
+ }
+ return
+}
+
+type storedExtent struct {
+ cache blockCache
+ locator string
+ offset int
+ length int
+}
+
+func (se storedExtent) Len() int64 {
+ return int64(se.length)
+}
+
+func (se storedExtent) ReadAt(p []byte, off int64) (n int, err error) {
+ maxlen := int(int64(se.length) - int64(se.offset) - off)
+ if len(p) > maxlen {
+ p = p[:maxlen]
+ n, err = se.cache.ReadAt(se.locator, p, off+int64(se.offset))
+ if err == nil {
+ err = io.EOF
}
- })
- return c.sizes
+ return
+ }
+ return se.cache.ReadAt(se.locator, p, off+int64(se.offset))
+}
+
+type blockCache interface {
+ ReadAt(locator string, p []byte, off int64) (n int, err error)
+}
+
+type keepBlockCache struct {
+ kc keepClient
+}
+
+var scratch = make([]byte, 2<<26)
+
+func (kbc *keepBlockCache) ReadAt(locator string, p []byte, off int64) (int, error) {
+ return kbc.kc.ReadAt(locator, p, off)
}
func canonicalName(name string) string {
@@ -278,3 +657,21 @@ func canonicalName(name string) string {
}
return name
}
+
+var manifestEscapeSeq = regexp.MustCompile(`\\([0-9]{3}|\\)`)
+
+func manifestUnescapeSeq(seq string) string {
+ if seq == `\\` {
+ return `\`
+ }
+ i, err := strconv.ParseUint(seq[1:], 8, 8)
+ if err != nil {
+ // Invalid escape sequence: can't unescape.
+ return seq
+ }
+ return string([]byte{byte(i)})
+}
+
+func manifestUnescape(s string) string {
+ return manifestEscapeSeq.ReplaceAllStringFunc(s, manifestUnescapeSeq)
+}
diff --git a/sdk/go/arvados/collection_fs_test.go b/sdk/go/arvados/collection_fs_test.go
index f51d1eb..7bd3570 100644
--- a/sdk/go/arvados/collection_fs_test.go
+++ b/sdk/go/arvados/collection_fs_test.go
@@ -16,17 +16,39 @@ import (
var _ = check.Suite(&CollectionFSSuite{})
+type keepClientStub struct {
+ blocks map[string][]byte
+}
+
+func (kcs *keepClientStub) ReadAt(locator string, p []byte, off int64) (int, error) {
+ buf := kcs.blocks[locator[:32]]
+ if buf == nil {
+ return 0, os.ErrNotExist
+ }
+ return copy(p, buf[int(off):]), nil
+}
+
type CollectionFSSuite struct {
client *Client
coll Collection
- fs http.FileSystem
+ fs CollectionFileSystem
+ kc keepClient
}
func (s *CollectionFSSuite) SetUpTest(c *check.C) {
s.client = NewClientFromEnv()
err := s.client.RequestAndDecode(&s.coll, "GET", "arvados/v1/collections/"+arvadostest.FooAndBarFilesInDirUUID, nil, nil)
c.Assert(err, check.IsNil)
- s.fs = s.coll.FileSystem(s.client, nil)
+ s.kc = &keepClientStub{
+ blocks: map[string][]byte{
+ "3858f62230ac3c915f300c664312c63f": []byte("foobar"),
+ }}
+ s.fs = s.coll.FileSystem(s.client, s.kc)
+}
+
+func (s *CollectionFSSuite) TestHttpFileSystemInterface(c *check.C) {
+ _, ok := s.fs.(http.FileSystem)
+ c.Check(ok, check.Equals, true)
}
func (s *CollectionFSSuite) TestReaddirFull(c *check.C) {
@@ -58,7 +80,7 @@ func (s *CollectionFSSuite) TestReaddirLimited(c *check.C) {
}
fis, err = f.Readdir(1)
- c.Check(err, check.Equals, io.EOF)
+ c.Check(err, check.IsNil)
c.Check(len(fis), check.Equals, 1)
if len(fis) > 0 {
c.Check(fis[0].Size(), check.Equals, int64(3))
@@ -76,7 +98,7 @@ func (s *CollectionFSSuite) TestReaddirLimited(c *check.C) {
c.Assert(err, check.IsNil)
fis, err = f.Readdir(2)
c.Check(len(fis), check.Equals, 1)
- c.Assert(err, check.Equals, io.EOF)
+ c.Assert(err, check.IsNil)
fis, err = f.Readdir(2)
c.Check(len(fis), check.Equals, 0)
c.Assert(err, check.Equals, io.EOF)
diff --git a/sdk/go/keepclient/block_cache.go b/sdk/go/keepclient/block_cache.go
index e841a00..c1138fa 100644
--- a/sdk/go/keepclient/block_cache.go
+++ b/sdk/go/keepclient/block_cache.go
@@ -49,6 +49,19 @@ func (c *BlockCache) Sweep() {
}
}
+// ReadAt returns data from the cache, first retrieving it from Keep if
+// necessary.
+func (c *BlockCache) ReadAt(kc *KeepClient, locator string, p []byte, off int64) (int, error) {
+ buf, err := c.Get(kc, locator)
+ if err != nil {
+ return 0, err
+ }
+ if off > int64(len(buf)) {
+ return 0, io.ErrUnexpectedEOF
+ }
+ return copy(p, buf[int(off):]), nil
+}
+
// Get returns data from the cache, first retrieving it from Keep if
// necessary.
func (c *BlockCache) Get(kc *KeepClient, locator string) ([]byte, error) {
diff --git a/sdk/go/keepclient/collectionreader.go b/sdk/go/keepclient/collectionreader.go
index 57829aa..3f39aff 100644
--- a/sdk/go/keepclient/collectionreader.go
+++ b/sdk/go/keepclient/collectionreader.go
@@ -43,14 +43,7 @@ func (kc *KeepClient) CollectionFileReader(collection map[string]interface{}, fi
}
func (kc *KeepClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
- f := &file{
- kc: kc,
- }
- err := f.load(m, filename)
- if err != nil {
- return nil, err
- }
- return f, nil
+ return (&arvados.Collection{ManifestText: m.Text}).FileSystem(nil, kc).OpenFile(filename, os.O_RDONLY, 0)
}
type file struct {
diff --git a/sdk/go/keepclient/keepclient.go b/sdk/go/keepclient/keepclient.go
index cbfad81..c3d63ed 100644
--- a/sdk/go/keepclient/keepclient.go
+++ b/sdk/go/keepclient/keepclient.go
@@ -292,6 +292,12 @@ func (kc *KeepClient) Get(locator string) (io.ReadCloser, int64, string, error)
return kc.getOrHead("GET", locator)
}
+// ReadAt() retrieves a portion of block from the cache if it's
+// present, otherwise from the network.
+func (kc *KeepClient) ReadAt(locator string, p []byte, off int64) (int, error) {
+ return kc.cache().ReadAt(kc, locator, p, off)
+}
+
// Ask() verifies that a block with the given hash is available and
// readable, according to at least one Keep service. Unlike Get, it
// does not retrieve the data or verify that the data content matches
-----------------------------------------------------------------------
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