h3. Conditions of creating a Collection
-The @portable_data_hash@ and @manifest_text@ attributes must be provided when creating a Collection. The cryptographic digest of the supplied @manifest_text@ must match the supplied @portable_data_hash@.
+If a new @portable_data_hash@ is specified when creating or updating a Collection, it must match the cryptographic digest of the supplied @manifest_text@.
h3. Side effects of creating a Collection
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
|collection|object||query||
+|replace_files|object|Initialize files and directories using content from other collections|query||
+
+The new collection's content can be initialized by providing a @manifest_text@ key in the provided @collection@ object, or by using the @replace_files@ option (see "replace_files":#replace_files below).
h3. delete
|_. Argument |_. Type |_. Description |_. Location |_. Example |
{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
|collection|object||query||
+|replace_files|object|Delete and replace files and directories using content from other collections|query||
+
+The collection's content can be updated by providing a @manifest_text@ key in the provided @collection@ object, or by using the @replace_files@ option (see "replace_files":#replace_files below).
h3. untrash
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
{background:#ccffcc}.|uuid|string|The UUID of the Collection to get usage.|path||
+
+h2(#replace_files). Using "replace_files" to create/update collections
+
+The @replace_files@ option can be used with the @create@ and @update@ APIs to efficiently copy individual files and directory trees from other collections, and copy/rename/delete items within an existing collection, without transferring any file data.
+
+@replace_files@ keys indicate target paths in the new collection, and values specify sources that should be copied to the target paths.
+* Each target path must be an absolute canonical path beginning with @/@. It must not contain @.@ or @..@ components, consecutive @/@ characters, or a trailing @/@ after the final component.
+* Each source must be either an empty string (signifying that the target path is to be deleted), or @PDH/path@ where @PDH@ is the portable data hash of a collection on the cluster and @/path@ is a file or directory in that collection.
+* In an @update@ request, sources may reference the current portable data hash of the collection being updated.
+
+Example: delete @foo.txt@ from a collection
+
+<notextile><pre>
+"replace_files": {
+ "/foo.txt": ""
+}
+</pre></notextile>
+
+Example: rename @foo.txt@ to @bar.txt@ in a collection with portable data hash @fa7aeb5140e2848d39b416daeef4ffc5+45@
+
+<notextile><pre>
+"replace_files": {
+ "/foo.txt": "",
+ "/bar.txt": "fa7aeb5140e2848d39b416daeef4ffc5+45/foo.txt"
+}
+</pre></notextile>
+
+Example: delete current contents, then add content from multiple collections
+
+<notextile><pre>
+"replace_files": {
+ "/": "",
+ "/copy of collection 1": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/",
+ "/copy of collection 2": "ea10d51bcf88862dbcc36eb292017dfd+45/"
+}
+</pre></notextile>
+
+Example: replace entire collection with a copy of a subdirectory from another collection
+
+<notextile><pre>
+"replace_files": {
+ "/": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/subdir"
+}
+</pre></notextile>
+
+A target path with a non-empty source cannot be the ancestor of another target path in the same request. For example, the following request is invalid:
+
+<notextile><pre>
+"replace_files": {
+ "/foo": "fa7aeb5140e2848d39b416daeef4ffc5+45/",
+ "/foo/this_will_return_an_error": ""
+}
+</pre></notextile>
import (
"context"
+ "fmt"
+ "net/http"
+ "os"
+ "sort"
+ "strings"
"time"
"git.arvados.org/arvados.git/sdk/go/arvados"
+ "git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/auth"
+ "git.arvados.org/arvados.git/sdk/go/httpserver"
)
// CollectionGet defers to railsProxy for everything except blob
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
+ if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, "", opts.Attrs, opts.ReplaceFiles); err != nil {
+ return arvados.Collection{}, err
+ }
resp, err := conn.railsProxy.CollectionCreate(ctx, opts)
if err != nil {
return resp, err
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
+ if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, opts.UUID, opts.Attrs, opts.ReplaceFiles); err != nil {
+ return arvados.Collection{}, err
+ }
resp, err := conn.railsProxy.CollectionUpdate(ctx, opts)
if err != nil {
return resp, err
}
coll.ManifestText = arvados.SignManifest(coll.ManifestText, token, exp, ttl, []byte(conn.cluster.Collections.BlobSigningKey))
}
+
+// If replaceFiles is non-empty, populate attrs["manifest_text"] by
+// starting with the content of fromUUID (or an empty collection if
+// fromUUID is empty) and applying the specified file/directory
+// replacements.
+//
+// Return value is the (possibly modified) attrs map.
+func (conn *Conn) applyReplaceFilesOption(ctx context.Context, fromUUID string, attrs map[string]interface{}, replaceFiles map[string]string) (map[string]interface{}, error) {
+ if len(replaceFiles) == 0 {
+ return attrs, nil
+ } else if mtxt, ok := attrs["manifest_text"].(string); ok && len(mtxt) > 0 {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "ambiguous request: both 'replace_files' and attrs['manifest_text'] values provided")
+ }
+
+ // Load the current collection (if any) and set up an
+ // in-memory filesystem.
+ var dst arvados.Collection
+ if _, replacingRoot := replaceFiles["/"]; !replacingRoot && fromUUID != "" {
+ src, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: fromUUID})
+ if err != nil {
+ return nil, err
+ }
+ dst = src
+ }
+ dstfs, err := dst.FileSystem(&arvados.StubClient{}, &arvados.StubClient{})
+ if err != nil {
+ return nil, err
+ }
+
+ // Sort replacements by source collection to avoid redundant
+ // reloads when a source collection is used more than
+ // once. Note empty sources (which mean "delete target path")
+ // sort first.
+ dstTodo := make([]string, 0, len(replaceFiles))
+ {
+ srcid := make(map[string]string, len(replaceFiles))
+ for dst, src := range replaceFiles {
+ dstTodo = append(dstTodo, dst)
+ if i := strings.IndexRune(src, '/'); i > 0 {
+ srcid[dst] = src[:i]
+ }
+ }
+ sort.Slice(dstTodo, func(i, j int) bool {
+ return srcid[dstTodo[i]] < srcid[dstTodo[j]]
+ })
+ }
+
+ // Reject attempt to replace a node as well as its descendant
+ // (e.g., a/ and a/b/), which is unsupported, except where the
+ // source for a/ is empty (i.e., delete).
+ for _, dst := range dstTodo {
+ if dst != "/" && (strings.HasSuffix(dst, "/") ||
+ strings.HasSuffix(dst, "/.") ||
+ strings.HasSuffix(dst, "/..") ||
+ strings.Contains(dst, "//") ||
+ strings.Contains(dst, "/./") ||
+ strings.Contains(dst, "/../") ||
+ !strings.HasPrefix(dst, "/")) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "invalid replace_files target: %q", dst)
+ }
+ for i := 0; i < len(dst)-1; i++ {
+ if dst[i] != '/' {
+ continue
+ }
+ outerdst := dst[:i]
+ if outerdst == "" {
+ outerdst = "/"
+ }
+ if outersrc := replaceFiles[outerdst]; outersrc != "" {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "replace_files: cannot operate on target %q inside non-empty target %q", dst, outerdst)
+ }
+ }
+ }
+
+ var srcidloaded string
+ var srcfs arvados.FileSystem
+ // Apply the requested replacements.
+ for _, dst := range dstTodo {
+ src := replaceFiles[dst]
+ if src == "" {
+ if dst == "/" {
+ // In this case we started with a
+ // blank manifest, so there can't be
+ // anything to delete.
+ continue
+ }
+ err := dstfs.RemoveAll(dst)
+ if err != nil {
+ return nil, fmt.Errorf("RemoveAll(%s): %w", dst, err)
+ }
+ continue
+ }
+ srcspec := strings.SplitN(src, "/", 2)
+ srcid, srcpath := srcspec[0], "/"
+ if !arvadosclient.PDHMatch(srcid) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "invalid source %q for replace_files[%q]: must be \"\" or \"PDH\" or \"PDH/path\"", src, dst)
+ }
+ if len(srcspec) == 2 && srcspec[1] != "" {
+ srcpath = srcspec[1]
+ }
+ if srcidloaded != srcid {
+ srcfs = nil
+ srccoll, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: srcid})
+ if err != nil {
+ return nil, err
+ }
+ // We use StubClient here because we don't
+ // want srcfs to read/write any file data or
+ // sync collection state to/from the database.
+ srcfs, err = srccoll.FileSystem(&arvados.StubClient{}, &arvados.StubClient{})
+ if err != nil {
+ return nil, err
+ }
+ srcidloaded = srcid
+ }
+ snap, err := arvados.Snapshot(srcfs, srcpath)
+ if err != nil {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "error getting snapshot of %q from %q: %w", srcpath, srcid, err)
+ }
+ // Create intermediate dirs, in case dst is
+ // "newdir1/newdir2/dst".
+ for i := 1; i < len(dst)-1; i++ {
+ if dst[i] == '/' {
+ err = dstfs.Mkdir(dst[:i], 0777)
+ if err != nil && !os.IsExist(err) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "error creating parent dirs for %q: %w", dst, err)
+ }
+ }
+ }
+ err = arvados.Splice(dstfs, dst, snap)
+ if err != nil {
+ return nil, fmt.Errorf("error splicing snapshot onto path %q: %w", dst, err)
+ }
+ }
+ mtxt, err := dstfs.MarshalManifest(".")
+ if err != nil {
+ return nil, err
+ }
+ if attrs == nil {
+ attrs = make(map[string]interface{}, 1)
+ }
+ attrs["manifest_text"] = mtxt
+ return attrs, nil
+}
import (
"context"
+ "io/fs"
+ "path/filepath"
"regexp"
+ "sort"
"strconv"
+ "strings"
"time"
"git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/controller/rpc"
"git.arvados.org/arvados.git/sdk/go/arvados"
+ "git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/arvadostest"
"git.arvados.org/arvados.git/sdk/go/auth"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "git.arvados.org/arvados.git/sdk/go/keepclient"
check "gopkg.in/check.v1"
)
s.localdb.vocabularyCache = voc
}
-func (s *CollectionSuite) TestCollectionCreateWithProperties(c *check.C) {
+func (s *CollectionSuite) TestCollectionCreateAndUpdateWithProperties(c *check.C) {
s.setUpVocabulary(c, "")
ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
for _, tt := range tests {
c.Log(c.TestName()+" ", tt.name)
+ // Create with properties
coll, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
Select: []string{"uuid", "properties"},
Attrs: map[string]interface{}{
} else {
c.Assert(err, check.NotNil)
}
- }
-}
-
-func (s *CollectionSuite) TestCollectionUpdateWithProperties(c *check.C) {
- s.setUpVocabulary(c, "")
- ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
- tests := []struct {
- name string
- props map[string]interface{}
- success bool
- }{
- {"Invalid prop key", map[string]interface{}{"Priority": "IDVALIMPORTANCES1"}, false},
- {"Invalid prop value", map[string]interface{}{"IDTAGIMPORTANCES": "high"}, false},
- {"Valid prop key & value", map[string]interface{}{"IDTAGIMPORTANCES": "IDVALIMPORTANCES1"}, true},
- {"Empty properties", map[string]interface{}{}, true},
- }
- for _, tt := range tests {
- c.Log(c.TestName()+" ", tt.name)
- coll, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{})
+ // Create, then update with properties
+ coll, err = s.localdb.CollectionCreate(ctx, arvados.CreateOptions{})
c.Assert(err, check.IsNil)
coll, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
UUID: coll.UUID,
}
}
+func (s *CollectionSuite) TestCollectionReplaceFiles(c *check.C) {
+ ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.AdminToken}})
+ foo, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &foo)
+ foobarbaz, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": "./foo/bar 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &foobarbaz)
+ wazqux, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": "./waz d85b1213473c2fd7c2045020a6b9c62b+3 0:3:qux.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &wazqux)
+
+ ctx = auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
+
+ // Create using content from existing collections
+ dst, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
+ ReplaceFiles: map[string]string{
+ "/f": foo.PortableDataHash + "/foo.txt",
+ "/b": foobarbaz.PortableDataHash + "/foo/bar",
+ "/q": wazqux.PortableDataHash + "/",
+ "/w": wazqux.PortableDataHash + "/waz",
+ },
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "f", "b/baz.txt", "q/waz/qux.txt", "w/qux.txt")
+
+ // Delete a file and a directory
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ "/f": "",
+ "/q/waz": "",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/baz.txt", "q/", "w/qux.txt")
+
+ // Move and copy content within collection
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ // Note splicing content to /b/corge.txt but
+ // removing everything else from /b
+ "/b": "",
+ "/b/corge.txt": dst.PortableDataHash + "/b/baz.txt",
+ "/quux/corge.txt": dst.PortableDataHash + "/b/baz.txt",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/corge.txt", "q/", "w/qux.txt", "quux/corge.txt")
+
+ // Remove everything except one file
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ "/": "",
+ "/b/corge.txt": dst.PortableDataHash + "/b/corge.txt",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/corge.txt")
+
+ // Copy entire collection to root
+ dstcopy, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
+ ReplaceFiles: map[string]string{
+ "/": dst.PortableDataHash,
+ }})
+ c.Check(err, check.IsNil)
+ c.Check(dstcopy.PortableDataHash, check.Equals, dst.PortableDataHash)
+ s.expectFiles(c, dstcopy, "b/corge.txt")
+
+ // Check invalid targets, sources, and combinations
+ for _, badrepl := range []map[string]string{
+ {
+ "/foo/nope": dst.PortableDataHash + "/b",
+ "/foo": dst.PortableDataHash + "/b",
+ },
+ {
+ "/foo": dst.PortableDataHash + "/b",
+ "/foo/nope": "",
+ },
+ {
+ "/": dst.PortableDataHash + "/",
+ "/nope": "",
+ },
+ {
+ "/": dst.PortableDataHash + "/",
+ "/nope": dst.PortableDataHash + "/b",
+ },
+ {"/bad/": ""},
+ {"/./bad": ""},
+ {"/b/./ad": ""},
+ {"/b/../ad": ""},
+ {"/b/.": ""},
+ {".": ""},
+ {"bad": ""},
+ {"": ""},
+ {"/bad": "/b"},
+ {"/bad": "bad/b"},
+ {"/bad": dst.UUID + "/b"},
+ } {
+ _, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: badrepl,
+ })
+ c.Logf("badrepl %#v\n... got err: %s", badrepl, err)
+ c.Check(err, check.NotNil)
+ }
+
+ // Check conflicting replace_files and manifest_text
+ _, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{"/": ""},
+ Attrs: map[string]interface{}{
+ "manifest_text": ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:z\n",
+ }})
+ c.Logf("replace_files+manifest_text\n... got err: %s", err)
+ c.Check(err, check.ErrorMatches, "ambiguous request: both.*replace_files.*manifest_text.*")
+}
+
+// expectFiles checks coll's directory structure against the given
+// list of expected files and empty directories. An expected path with
+// a trailing slash indicates an empty directory.
+func (s *CollectionSuite) expectFiles(c *check.C, coll arvados.Collection, expected ...string) {
+ client := arvados.NewClientFromEnv()
+ ac, err := arvadosclient.New(client)
+ c.Assert(err, check.IsNil)
+ kc, err := keepclient.MakeKeepClient(ac)
+ c.Assert(err, check.IsNil)
+ cfs, err := coll.FileSystem(arvados.NewClientFromEnv(), kc)
+ c.Assert(err, check.IsNil)
+ var found []string
+ nonemptydirs := map[string]bool{}
+ fs.WalkDir(arvados.FS(cfs), "/", func(path string, d fs.DirEntry, err error) error {
+ dir, _ := filepath.Split(path)
+ nonemptydirs[dir] = true
+ if d.IsDir() {
+ if path != "/" {
+ path += "/"
+ }
+ if !nonemptydirs[path] {
+ nonemptydirs[path] = false
+ }
+ } else {
+ found = append(found, path)
+ }
+ return nil
+ })
+ for d, nonempty := range nonemptydirs {
+ if !nonempty {
+ found = append(found, d)
+ }
+ }
+ for i, path := range found {
+ if path != "/" {
+ found[i] = strings.TrimPrefix(path, "/")
+ }
+ }
+ sort.Strings(found)
+ sort.Strings(expected)
+ c.Check(found, check.DeepEquals, expected)
+}
+
func (s *CollectionSuite) TestSignatures(c *check.C) {
ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
def test_small_collection
uuid = Digest::MD5.hexdigest(foo_manifest) + '+' + foo_manifest.size.to_s
+ ok = nil
out, err = capture_subprocess_io do
- assert_arv('--format', 'uuid', 'collection', 'create', '--collection', {
- uuid: uuid,
- manifest_text: foo_manifest
- }.to_json)
+ ok = arv('--format', 'uuid', 'collection', 'create', '--collection', {
+ uuid: uuid,
+ manifest_text: foo_manifest
+ }.to_json)
end
- assert(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(out))
- assert_equal '', err
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, out)
+ end
+
+ def test_collection_replace_files
+ ok = nil
+ uuid, err = capture_subprocess_io do
+ ok = arv('--format', 'uuid', 'collection', 'create', '--collection', '{}')
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, uuid)
+ uuid = uuid.strip
+
+ out, err = capture_subprocess_io do
+ ok = arv('--format', 'uuid',
+ 'collection', 'update',
+ '--uuid', uuid,
+ '--collection', '{}',
+ '--replace-files', {
+ "/gpl.pdf": "b519d9cb706a29fc7ea24dbea2f05851+93/GNU_General_Public_License,_version_3.pdf",
+ }.to_json)
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_equal(uuid, out.strip)
+
+ ok = nil
+ out, err = capture_subprocess_io do
+ ok = arv('--format', 'json', 'collection', 'get', '--uuid', uuid)
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/\. 6a4ff0499484c6c79c95cd8c566bd25f\+249025.* 0:249025:gpl.pdf\\n/, out)
end
def test_read_resource_object_from_file
begin
tempfile.write({manifest_text: foo_manifest}.to_json)
tempfile.close
+ ok = nil
out, err = capture_subprocess_io do
- assert_arv('--format', 'uuid',
- 'collection', 'create', '--collection', tempfile.path)
+ ok = arv('--format', 'uuid',
+ 'collection', 'create', '--collection', tempfile.path)
end
- assert(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(out))
- assert_equal '', err
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, out)
ensure
tempfile.unlink
end
end
protected
- def assert_arv(*args)
- expect = case args.first
- when true, false
- args.shift
- else
- true
- end
- assert_equal(expect,
- system(['./bin/arv', 'arv'], *args),
- "`arv #{args.join ' '}` " +
- "should exit #{if expect then 0 else 'non-zero' end}")
+ def arv(*args)
+ system(['./bin/arv', 'arv'], *args)
end
def foo_manifest
EnsureUniqueName bool `json:"ensure_unique_name"`
Select []string `json:"select"`
Attrs map[string]interface{} `json:"attrs"`
+ // ReplaceFiles only applies when creating a collection.
+ ReplaceFiles map[string]string `json:"replace_files"`
}
type UpdateOptions struct {
Attrs map[string]interface{} `json:"attrs"`
Select []string `json:"select"`
BypassFederation bool `json:"bypass_federation"`
+ // ReplaceFiles only applies when updating a collection.
+ ReplaceFiles map[string]string `json:"replace_files"`
}
type GroupContentsOptions struct {
import (
"context"
+ "errors"
"io"
)
type apiClient interface {
RequestAndDecode(dst interface{}, method, path string, body io.Reader, params interface{}) error
}
+
+var errStubClient = errors.New("stub client")
+
+type StubClient struct{}
+
+func (*StubClient) ReadAt(string, []byte, int) (int, error) { return 0, errStubClient }
+func (*StubClient) LocalLocator(loc string) (string, error) { return loc, nil }
+func (*StubClient) BlockWrite(context.Context, BlockWriteOptions) (BlockWriteResponse, error) {
+ return BlockWriteResponse{}, errStubClient
+}
+func (*StubClient) RequestAndDecode(_ interface{}, _, _ string, _ io.Reader, _ interface{}) error {
+ return errStubClient
+}
"errors"
"fmt"
"io"
+ "io/fs"
"log"
"net/http"
"os"
MemorySize() int64
}
+type fsFS struct {
+ FileSystem
+}
+
+// FS returns an fs.FS interface to the given FileSystem, to enable
+// the use of fs.WalkDir, etc.
+func FS(fs FileSystem) fs.FS { return fsFS{fs} }
+func (fs fsFS) Open(path string) (fs.File, error) {
+ f, err := fs.FileSystem.Open(path)
+ return f, err
+}
+
type inode interface {
SetParent(parent inode, name string)
Parent() inode
default:
return nil, fmt.Errorf("invalid flags 0x%x", flag)
}
- if !writable && parent.IsDir() {
+ if parent.IsDir() {
// A directory can be opened via "foo/", "foo/.", or
// "foo/..".
switch name {
case ".", "":
- return &filehandle{inode: parent}, nil
+ return &filehandle{inode: parent, readable: readable, writable: writable}, nil
case "..":
- return &filehandle{inode: parent.Parent()}, nil
+ return &filehandle{inode: parent.Parent(), readable: readable, writable: writable}, nil
}
}
createMode := flag&os.O_CREATE != 0
f, err = fs.OpenFile(target, os.O_CREATE|os.O_WRONLY, 0700)
}
if err != nil {
- return err
+ return fmt.Errorf("open %s: %w", target, err)
}
defer f.Close()
return f.Splice(newsubtree)
func (dn *dirnode) Splice(repl inode) error {
repl, err := repl.Snapshot()
if err != nil {
- return err
+ return fmt.Errorf("cannot copy snapshot: %w", err)
}
switch repl := repl.(type) {
default:
defer dn.Unlock()
_, err = dn.parent.Child(dn.fileinfo.name, func(inode) (inode, error) { return repl, nil })
if err != nil {
- return err
+ return fmt.Errorf("error replacing filenode: dn.parent.Child(): %w", err)
}
repl.fs = dn.fs
}
}
}
+func (s *CollectionFSSuite) TestSnapshotSplice(c *check.C) {
+ filedata1 := "hello snapshot+splice world\n"
+ fs, err := (&Collection{}).FileSystem(s.client, s.kc)
+ c.Assert(err, check.IsNil)
+ {
+ f, err := fs.OpenFile("file1", os.O_CREATE|os.O_RDWR, 0700)
+ c.Assert(err, check.IsNil)
+ _, err = f.Write([]byte(filedata1))
+ c.Assert(err, check.IsNil)
+ err = f.Close()
+ c.Assert(err, check.IsNil)
+ }
+
+ snap, err := Snapshot(fs, "/")
+ c.Assert(err, check.IsNil)
+ err = Splice(fs, "dir1", snap)
+ c.Assert(err, check.IsNil)
+ f, err := fs.Open("dir1/file1")
+ c.Assert(err, check.IsNil)
+ buf, err := io.ReadAll(f)
+ c.Assert(err, check.IsNil)
+ c.Check(string(buf), check.Equals, filedata1)
+}
+
func (s *CollectionFSSuite) TestRefreshSignatures(c *check.C) {
filedata1 := "hello refresh signatures world\n"
fs, err := (&Collection{}).FileSystem(s.client, s.kc)
import (
"io"
+ "io/fs"
"os"
)
return
}
+// dirEntry implements fs.DirEntry, see (*filehandle)ReadDir().
+type dirEntry struct {
+ os.FileInfo
+}
+
+func (ent dirEntry) Type() fs.FileMode {
+ return ent.Mode().Type()
+}
+func (ent dirEntry) Info() (fs.FileInfo, error) {
+ return ent, nil
+}
+
+// ReadDir implements fs.ReadDirFile.
+func (f *filehandle) ReadDir(count int) ([]fs.DirEntry, error) {
+ fis, err := f.Readdir(count)
+ if len(fis) == 0 {
+ return nil, err
+ }
+ ents := make([]fs.DirEntry, len(fis))
+ for i, fi := range fis {
+ ents[i] = dirEntry{fi}
+ }
+ return ents, err
+}
+
func (f *filehandle) Readdir(count int) ([]os.FileInfo, error) {
if !f.inode.IsDir() {
return nil, ErrInvalidOperation
"io/ioutil"
"net/http"
"os"
+ "strings"
"syscall"
"time"
c.Check(string(buf), check.Equals, string(thisfile))
}
- // Cannot splice a file onto a collection root, or anywhere
- // outside a collection
+ // Cannot splice a file onto a collection root; cannot splice
+ // anything to a target outside a collection.
for _, badpath := range []string{
+ dstPath + "/",
dstPath,
+ "/home/A Project/newnodename/",
"/home/A Project/newnodename",
+ "/home/A Project/",
"/home/A Project",
+ "/home/newnodename/",
"/home/newnodename",
+ "/home/",
"/home",
+ "/newnodename/",
"/newnodename",
+ "/",
} {
err = Splice(s.fs, badpath, snapFile)
c.Check(err, check.NotNil)
- c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %s"))
- if badpath == dstPath {
- c.Check(err, check.ErrorMatches, `cannot use Splice to attach a file at top level of \*arvados.collectionFileSystem: invalid operation`, check.Commentf("badpath: %s", badpath))
+ if strings.Contains(badpath, "newnodename") && strings.HasSuffix(badpath, "/") {
+ c.Check(err, ErrorIs, os.ErrNotExist, check.Commentf("badpath %q", badpath))
+ } else {
+ c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %q", badpath))
+ }
+ if strings.TrimSuffix(badpath, "/") == dstPath {
+ c.Check(err, check.ErrorMatches, `cannot use Splice to attach a file at top level of \*arvados.collectionFileSystem: invalid operation`, check.Commentf("badpath: %q", badpath))
continue
}
- err = Splice(s.fs, badpath, snap1)
- c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %s"))
- }
- // Destination cannot have trailing slash
- for _, badpath := range []string{
- dstPath + "/ctxlog/",
- dstPath + "/",
- "/home/A Project/",
- "/home/",
- "/",
- "",
- } {
err = Splice(s.fs, badpath, snap1)
- c.Check(err, ErrorIs, ErrInvalidArgument, check.Commentf("badpath %s", badpath))
- err = Splice(s.fs, badpath, snapFile)
- c.Check(err, ErrorIs, ErrInvalidArgument, check.Commentf("badpath %s", badpath))
+ if strings.Contains(badpath, "newnodename") && strings.HasSuffix(badpath, "/") {
+ c.Check(err, ErrorIs, os.ErrNotExist, check.Commentf("badpath %q", badpath))
+ } else {
+ c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %q", badpath))
+ }
}
// Destination's parent must already exist
}
snap2, err := Snapshot(s.fs, dstPath+"/ctxlog-copy")
- c.Check(err, check.IsNil)
- err = Splice(s.fs, dstPath+"/ctxlog-copy-copy", snap2)
- c.Check(err, check.IsNil)
+ if c.Check(err, check.IsNil) {
+ err = Splice(s.fs, dstPath+"/ctxlog-copy-copy", snap2)
+ c.Check(err, check.IsNil)
+ }
// Snapshot entire collection, splice into same collection at
// a new path, remove file from original location, verify
_, err = s.fs.Open(dstPath + "/arvados/fs_site_test.go")
c.Check(err, check.Equals, os.ErrNotExist)
f, err = s.fs.Open(dstPath + "/copy2/arvados/fs_site_test.go")
- c.Check(err, check.IsNil)
- defer f.Close()
- buf, err := ioutil.ReadAll(f)
- c.Check(err, check.IsNil)
- c.Check(string(buf), check.Equals, string(thisfile))
+ if c.Check(err, check.IsNil) {
+ defer f.Close()
+ buf, err := ioutil.ReadAll(f)
+ c.Check(err, check.IsNil)
+ c.Check(string(buf), check.Equals, string(thisfile))
+ }
}
import (
"encoding/json"
+ "fmt"
"net/http"
)
+func Errorf(status int, tmpl string, args ...interface{}) error {
+ return errorWithStatus{fmt.Errorf(tmpl, args...), status}
+}
+
func ErrorWithStatus(err error, status int) error {
return errorWithStatus{err, status}
}
end
end
+ # The 'replace_files' option is implemented in lib/controller,
+ # not Rails -- we just need to add it here so discovery-aware
+ # clients know how to validate it.
+ [:create, :update].each do |action|
+ discovery[:resources]['collections'][:methods][action][:parameters]['replace_files'] = {
+ type: 'object',
+ description: 'Files and directories to initialize/replace with content from other collections.',
+ required: false,
+ location: 'query',
+ properties: {},
+ additionalProperties: {type: 'string'},
+ }
+ end
+
discovery[:resources]['configs'] = {
methods: {
get: {
projects / arvados.git / commitdiff