[ARVADOS] updated: 2.1.0-2013-ge62689fb8
Git user
git at public.arvados.org
Thu Mar 10 20:27:46 UTC 2022
Summary of changes:
doc/api/methods/collections.html.textile.liquid | 54 ++++++-------
lib/controller/localdb/collection.go | 94 +++++++++-------------
lib/controller/localdb/collection_test.go | 92 +++++++--------------
sdk/go/arvados/api.go | 4 +
.../controllers/arvados/v1/schema_controller.rb | 11 +++
5 files changed, 106 insertions(+), 149 deletions(-)
via e62689fb8f8e12bb72632463668bf6ea8cbb9662 (commit)
from f00d666fdf3f4322a6e153a9dc3a25069859e52d (commit)
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commit e62689fb8f8e12bb72632463668bf6ea8cbb9662
Author: Tom Clegg <tom at curii.com>
Date: Thu Mar 10 15:25:41 2022 -0500
18600: Move "splices" to "update_files" update/create option.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/doc/api/methods/collections.html.textile.liquid b/doc/api/methods/collections.html.textile.liquid
index bea19bb75..ea67937e8 100644
--- a/doc/api/methods/collections.html.textile.liquid
+++ b/doc/api/methods/collections.html.textile.liquid
@@ -71,9 +71,10 @@ Arguments:
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
-|collection|object||query||
+|collection|object||body||
+|replace_files|object|Initialize files and directories using content from other collections|body||
-The new collection's content can be initialized by providing a @manifest_text@ or @splices@ key in the provided @collection@ object (see "splices":#splices below).
+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
@@ -117,9 +118,10 @@ Arguments:
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
-|collection|object||query||
+|collection|object||body||
+|replace_files|object|Delete and replace files and directories using content from other collections|body||
-The collection's content can be updated by providing a @manifest_text@ or @splices@ key in the provided @collection@ object (see "splices":#splices below).
+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
@@ -165,11 +167,11 @@ 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(#splices). Using "splices" to create/update collections
+h2(#replace_files). Using "replace_files" to create/update collections
-The @splices@ attribute 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.
+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.
- at splices@ keys indicate target paths in the new collection, and values specify sources that should be copied to the target paths.
+ at 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.
@@ -177,53 +179,43 @@ The @splices@ attribute can be used with the @create@ and @update@ APIs to effic
Example: delete @foo.txt@ from a collection
<notextile><pre>
-"collection": {
- "splices": {
- "/foo.txt": ""
- }
+"replace_files": {
+ "/foo.txt": ""
}
</pre></notextile>
Example: rename @foo.txt@ to @bar.txt@ in a collection with portable data hash @fa7aeb5140e2848d39b416daeef4ffc5+45@
<notextile><pre>
-"collection": {
- "splices": {
- "/foo.txt": "",
- "/bar.txt": "fa7aeb5140e2848d39b416daeef4ffc5+45/foo.txt"
- }
+"replace_files": {
+ "/foo.txt": "",
+ "/bar.txt": "fa7aeb5140e2848d39b416daeef4ffc5+45/foo.txt"
}
</pre></notextile>
Example: delete current contents, then add content from multiple collections
<notextile><pre>
-"collection": {
- "splices": {
- "/": "",
- "/copy of collection 1": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/",
- "/copy of collection 2": "ea10d51bcf88862dbcc36eb292017dfd+45/"
- }
+"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>
-"collection": {
- "splices": {
- "/": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/subdir"
- }
+"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>
-"collection": {
- "splices": {
- "/foo": "fa7aeb5140e2848d39b416daeef4ffc5+45/",
- "/foo/this_will_return_an_error": ""
- }
+"replace_files": {
+ "/foo": "fa7aeb5140e2848d39b416daeef4ffc5+45/",
+ "/foo/this_will_return_an_error": ""
}
</pre></notextile>
diff --git a/lib/controller/localdb/collection.go b/lib/controller/localdb/collection.go
index 2283b2fcb..868e466e9 100644
--- a/lib/controller/localdb/collection.go
+++ b/lib/controller/localdb/collection.go
@@ -68,7 +68,7 @@ func (conn *Conn) CollectionCreate(ctx context.Context, opts arvados.CreateOptio
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
- if err := conn.applySplices(ctx, "", opts.Attrs); err != nil {
+ if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, "", opts.Attrs, opts.ReplaceFiles); err != nil {
return arvados.Collection{}, err
}
resp, err := conn.railsProxy.CollectionCreate(ctx, opts)
@@ -92,7 +92,7 @@ func (conn *Conn) CollectionUpdate(ctx context.Context, opts arvados.UpdateOptio
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
- if err := conn.applySplices(ctx, opts.UUID, opts.Attrs); err != nil {
+ 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)
@@ -122,64 +122,42 @@ func (conn *Conn) signCollection(ctx context.Context, coll *arvados.Collection)
coll.ManifestText = arvados.SignManifest(coll.ManifestText, token, exp, ttl, []byte(conn.cluster.Collections.BlobSigningKey))
}
-// If attrs["splices"] is present, populate attrs["manifest_text"] by
+// 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 splice operations.
-func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[string]interface{}) error {
- var splices map[string]string
-
- // Validate the incoming attrs, and return early if the
- // request doesn't ask for any splices.
- if sp, ok := attrs["splices"]; !ok {
- return nil
- } else {
- switch sp := sp.(type) {
- default:
- return httpserver.Errorf(http.StatusBadRequest, "invalid type %T for splices parameter", sp)
- case nil:
- return nil
- case map[string]string:
- splices = sp
- case map[string]interface{}:
- splices = make(map[string]string, len(sp))
- for dst, src := range sp {
- if src, ok := src.(string); ok {
- splices[dst] = src
- } else {
- return httpserver.Errorf(http.StatusBadRequest, "invalid source type for splice target %q: %v", dst, src)
- }
- }
- }
- if len(splices) == 0 {
- return nil
- } else if mtxt, ok := attrs["manifest_text"].(string); ok && len(mtxt) > 0 {
- return httpserver.Errorf(http.StatusBadRequest, "ambiguous request: both 'splices' and 'manifest_text' values provided")
- }
+// 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 _, rootsplice := splices["/"]; !rootsplice && fromUUID != "" {
+ if _, replacingRoot := replaceFiles["/"]; !replacingRoot && fromUUID != "" {
src, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: fromUUID})
if err != nil {
- return err
+ return nil, err
}
dst = src
}
dstfs, err := dst.FileSystem(&arvados.StubClient{}, &arvados.StubClient{})
if err != nil {
- return err
+ return nil, err
}
- // Sort splices by source collection to avoid redundant
+ // 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(splices))
+ dstTodo := make([]string, 0, len(replaceFiles))
{
- srcid := make(map[string]string, len(splices))
- for dst, src := range splices {
+ 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]
@@ -190,7 +168,7 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
})
}
- // Reject attempt to splice a node as well as its descendant
+ // 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 {
@@ -201,7 +179,7 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
strings.Contains(dst, "/./") ||
strings.Contains(dst, "/../") ||
!strings.HasPrefix(dst, "/")) {
- return httpserver.Errorf(http.StatusBadRequest, "invalid splice target: %q", dst)
+ return nil, httpserver.Errorf(http.StatusBadRequest, "invalid replace_files target: %q", dst)
}
for i := 0; i < len(dst)-1; i++ {
if dst[i] != '/' {
@@ -211,17 +189,17 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
if outerdst == "" {
outerdst = "/"
}
- if outersrc := splices[outerdst]; outersrc != "" {
- return httpserver.Errorf(http.StatusBadRequest, "cannot splice at target %q with non-empty splice at %q", dst, 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 splices.
+ // Apply the requested replacements.
for _, dst := range dstTodo {
- src := splices[dst]
+ src := replaceFiles[dst]
if src == "" {
if dst == "/" {
// In this case we started with a
@@ -231,14 +209,14 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
}
err := dstfs.RemoveAll(dst)
if err != nil {
- return fmt.Errorf("RemoveAll(%s): %w", dst, err)
+ return nil, fmt.Errorf("RemoveAll(%s): %w", dst, err)
}
continue
}
srcspec := strings.SplitN(src, "/", 2)
srcid, srcpath := srcspec[0], "/"
if !arvadosclient.PDHMatch(srcid) {
- return httpserver.Errorf(http.StatusBadRequest, "invalid source %q for splices[%q]: must be \"\" or \"PDH\" or \"PDH/path\"", src, dst)
+ 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]
@@ -247,20 +225,20 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
srcfs = nil
srccoll, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: srcid})
if err != nil {
- return err
+ 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 err
+ return nil, err
}
srcidloaded = srcid
}
snap, err := arvados.Snapshot(srcfs, srcpath)
if err != nil {
- return httpserver.Errorf(http.StatusBadRequest, "error getting snapshot of %q from %q: %w", srcpath, srcid, err)
+ 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".
@@ -268,20 +246,22 @@ func (conn *Conn) applySplices(ctx context.Context, fromUUID string, attrs map[s
if dst[i] == '/' {
err = dstfs.Mkdir(dst[:i], 0777)
if err != nil && !os.IsExist(err) {
- return httpserver.Errorf(http.StatusBadRequest, "error creating parent dirs for %q: %w", dst, 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 fmt.Errorf("error splicing snapshot onto path %q: %w", dst, err)
+ return nil, fmt.Errorf("error splicing snapshot onto path %q: %w", dst, err)
}
}
mtxt, err := dstfs.MarshalManifest(".")
if err != nil {
- return err
+ return nil, err
+ }
+ if attrs == nil {
+ attrs = make(map[string]interface{}, 1)
}
- delete(attrs, "splices")
attrs["manifest_text"] = mtxt
- return nil
+ return attrs, nil
}
diff --git a/lib/controller/localdb/collection_test.go b/lib/controller/localdb/collection_test.go
index e71ae35c2..dac8b769f 100644
--- a/lib/controller/localdb/collection_test.go
+++ b/lib/controller/localdb/collection_test.go
@@ -125,7 +125,7 @@ func (s *CollectionSuite) TestCollectionCreateAndUpdateWithProperties(c *check.C
}
}
-func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
+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{}{
@@ -153,14 +153,14 @@ func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
// 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,
- "splices": map[string]string{
- "/f": foo.PortableDataHash + "/foo.txt",
- "/b": foobarbaz.PortableDataHash + "/foo/bar",
- "/q": wazqux.PortableDataHash + "/",
- "/w": wazqux.PortableDataHash + "/waz",
- },
}})
c.Assert(err, check.IsNil)
s.expectFiles(c, dst, "f", "b/baz.txt", "q/waz/qux.txt", "w/qux.txt")
@@ -168,11 +168,9 @@ func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
// Delete a file and a directory
dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
UUID: dst.UUID,
- Attrs: map[string]interface{}{
- "splices": map[string]string{
- "/f": "",
- "/q/waz": "",
- },
+ ReplaceFiles: map[string]string{
+ "/f": "",
+ "/q/waz": "",
}})
c.Assert(err, check.IsNil)
s.expectFiles(c, dst, "b/baz.txt", "q/", "w/qux.txt")
@@ -180,15 +178,12 @@ func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
// Move and copy content within collection
dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
UUID: dst.UUID,
- Attrs: map[string]interface{}{
- "splices": 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",
- },
+ 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")
@@ -196,31 +191,24 @@ func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
// Remove everything except one file
dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
UUID: dst.UUID,
- Attrs: map[string]interface{}{
- "splices": map[string]string{
- "/": "",
- "/b/corge.txt": dst.PortableDataHash + "/b/corge.txt",
- },
+ 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{
- Attrs: map[string]interface{}{
- // Note map[string]interface{} here, which is
- // how lib/controller/router requests will
- // look.
- "splices": map[string]interface{}{
- "/": dst.PortableDataHash,
- },
+ 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 _, splices := range []map[string]string{
+ for _, badrepl := range []map[string]string{
{
"/foo/nope": dst.PortableDataHash + "/b",
"/foo": dst.PortableDataHash + "/b",
@@ -250,40 +238,22 @@ func (s *CollectionSuite) TestCollectionUpdateFiles(c *check.C) {
{"/bad": dst.UUID + "/b"},
} {
_, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
- UUID: dst.UUID,
- Attrs: map[string]interface{}{
- "splices": splices,
- }})
- c.Logf("splices %#v\n... got err: %s", splices, err)
+ UUID: dst.UUID,
+ ReplaceFiles: badrepl,
+ })
+ c.Logf("badrepl %#v\n... got err: %s", badrepl, err)
c.Check(err, check.NotNil)
}
- // Check "splices" value that isn't even the right type
- for _, splices := range []interface{}{
- map[string]int{"foo": 1},
- map[int]string{1: "foo"},
- 12345,
- "foo",
- []string{"foo"},
- } {
- _, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
- UUID: dst.UUID,
- Attrs: map[string]interface{}{
- "splices": splices,
- }})
- c.Logf("splices %#v\n... got err: %s", splices, err)
- c.Check(err, check.ErrorMatches, "invalid type .* for splices parameter")
- }
-
- // Check conflicting splices and manifest_text
+ // Check conflicting replace_files and manifest_text
_, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
- UUID: dst.UUID,
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{"/": ""},
Attrs: map[string]interface{}{
- "splices": map[string]string{"/": ""},
"manifest_text": ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:z\n",
}})
- c.Logf("splices+manifest_text\n... got err: %s", err)
- c.Check(err, check.ErrorMatches, "ambiguous request: both.*splices.*manifest_text.*")
+ 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
diff --git a/sdk/go/arvados/api.go b/sdk/go/arvados/api.go
index 7409b1813..d76ece1ed 100644
--- a/sdk/go/arvados/api.go
+++ b/sdk/go/arvados/api.go
@@ -139,6 +139,8 @@ type CreateOptions struct {
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 {
@@ -146,6 +148,8 @@ 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 {
diff --git a/services/api/app/controllers/arvados/v1/schema_controller.rb b/services/api/app/controllers/arvados/v1/schema_controller.rb
index 59ac639ba..824df62e8 100644
--- a/services/api/app/controllers/arvados/v1/schema_controller.rb
+++ b/services/api/app/controllers/arvados/v1/schema_controller.rb
@@ -406,6 +406,17 @@ class Arvados::V1::SchemaController < ApplicationController
end
end
+ # The 'update_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][:request][:properties]['update_files'] = {
+ type: 'object',
+ properties: {},
+ additionalProperties: {type: 'string'},
+ }
+ end
+
discovery[:resources]['configs'] = {
methods: {
get: {
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