fix(dedupe): use a common blobs dir to simplify by rchincha · Pull Request #3314 · project-zot/zot

rchincha · 2025-08-17T05:19:53Z

Currently, our dedupe scheme is very complicated since master copy is kept in one of the repo dirs and if that image is deleted, the owning repo is changed, requiring multiple repo locks causing unnecessary contention.

What type of PR is this?

Which issue does this PR fix:

What does this PR do / Why do we need it:

If an issue # is not available please add repro steps and logs showing the issue:

Testing done on this change:

Automation added to e2e:

Will this break upgrades or downgrades?

Does this PR introduce any user-facing change?:

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

rchincha · 2025-08-19T16:06:41Z

Should pair with #2968

andaaron · 2025-09-04T16:35:00Z

 	DefaultGCInterval       = 1 * time.Hour
 	S3StorageDriverName     = "s3"
 	LocalStorageDriverName  = "local"
+	GlobalBlobsRepo         = "_blobstore"


Make sure this blobs repo is per store and substore. Because substores may be on different partitions.

andaaron

I think the logging is too verbose, and should be trimmed

andaaron · 2025-10-20T07:01:30Z

 			substore := c.StoreController.SubStore[route]
 			if substore != nil {
-				substore.RunDedupeBlobs(time.Duration(0), c.taskScheduler)
+				//substore.RunDedupeBlobs(time.Duration(0), c.taskScheduler)


Is this just temporary, or we're dropping dedupe altogether?

andaaron · 2025-10-20T07:06:05Z

+			return nil
+		}
+
+		// create nested deduped bucket where we store all the deduped blobs + original blob


Suggested change

// create nested deduped bucket where we store all the deduped blobs + original blob

// create nested deduped bucket where we store all the deduped blobs while excluding the original blob

Correct?

andaaron · 2025-10-20T07:11:00Z

I think the logging is too verbose for merge. It would be too much information to include logs for the code paths not returning errors.

andaaron · 2025-10-20T07:26:05Z

+
+				dedupeBlob := d.getOne(deduped)
+				if dedupeBlob != nil {
+					d.log.Debug().Str("digest", digest.String()).Str("path", path).Msg("more in dedupe bucket, leaving original alone")


Previous logic was replacing the old original blob with one of the duplicates, and then delete the blob.
This new logic would keep the original blob around forever? How/when would it be GCed?

andaaron · 2025-10-20T07:32:39Z

 		}

-		return nil
+		return zerr.ErrCacheMiss


Under which scenario would this return the error?
The updated code is a bit confusing as it is returning nil in several other places and it is unclear in which scenario this line is reached.

andaaron · 2025-10-20T07:37:32Z

Are there no other needed changes in this file?

Also the redis implementation should be reviewed

andaaron · 2025-10-20T07:41:14Z

 		}

 		origin := bucket.Bucket([]byte(constants.OriginalBucket))
 		if origin != nil {


And if origin is nil, then we should return nil, because the blob does not exist.

It is not in the duplicates list and it is not the original, so it does not exist, so the deletion should be marked as successful, correct?

andaaron · 2025-10-20T07:51:51Z

 	}

+	// skip the global blobs repo
+	if repo == constants.GlobalBlobsRepo {


Something is fishy.
Why is this here? constants.GlobalBlobsRepo is not an actual repo because it has an invalid repo name. How is GC detecting it when "walking" the disk if it doesn't have a valid repo name? It shouldn't call this function at all for constants.GlobalBlobsRepo?

andaaron · 2025-10-20T08:13:37Z


-				return err
-			}
+		goto retry


Since we're refactoring this, can you pick up #2969?
Or do you want me to rebase and merge that in advance?

Is this code working right now, wouldn't it potentially execute the code multiple times?

if err := is.storeDriver.Move(src, gdst); err != nil { is.log.Error().Err(err).Str("src", src).Str("dst", gdst).Str("component", "dedupe"). Msg("failed to rename blob") return err }

Copilot

Pull request overview

This PR refactors the deduplication scheme to simplify blob management by introducing a centralized global blob storage location (_blobstore) instead of maintaining master copies within individual repository directories. This eliminates complex repository ownership changes when images are deleted and reduces lock contention.

Key Changes:

Introduces a GlobalBlobsRepo constant (_blobstore) to serve as a centralized master copy location for all deduplicated blobs
Refactors validation logic by moving it from initRepo to InitRepo to allow internal initialization of the special global blobs repository
Updates cache deletion logic in BoltDB and DynamoDB drivers to handle the new deduplication scheme
Modifies garbage collection to include the global blobs repository

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
pkg/storage/constants/constants.go	Adds `GlobalBlobsRepo` constant defining the centralized blob storage location
pkg/storage/imagestore/imagestore.go	Refactors deduplication logic to use global blobs repo, moves validation from `initRepo` to `InitRepo`
pkg/storage/cache/boltdb.go	Updates cache deletion logic to check duplicates bucket first and handle global blob storage
pkg/storage/cache/dynamodb.go	Adds duplicate blob check before deletion in DynamoDB cache driver
pkg/storage/cache/boltdb_test.go	Updates test expectations for new cache behavior (contains debug statements)
pkg/storage/cache_test.go	Updates test expectations for cache deletion behavior
pkg/storage/storage_test.go	Adds GlobalBlobsRepo to test candidates list and skips it in image writing loop
pkg/storage/gc/gc.go	Adds garbage collection logic for global blobs repository (contains commented code and FIXMEs)
pkg/api/controller.go	Comments out `RunDedupeBlobs` calls (temporarily disabled functionality)

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Copilot · 2025-11-23T20:50:41Z


 	// Enable running dedupe blobs both ways (dedupe or restore deduped blobs)
-	c.StoreController.DefaultStore.RunDedupeBlobs(time.Duration(0), c.taskScheduler)
+	//	c.StoreController.DefaultStore.RunDedupeBlobs(time.Duration(0), c.taskScheduler)


Commented out dedupe functionality should be removed if it's no longer needed, or should have a clear comment explaining why it's temporarily disabled with a tracking issue reference.

Copilot · 2025-11-23T20:50:41Z

 }

 func (d *BoltDBDriver) HasBlob(digest godigest.Digest, blob string) bool {
+	d.log.Debug().Str("digest", digest.String()).Str("blob", "blob").Msg("checking blob in cache")


The parameter name "blob" is logged as the string literal "blob" instead of the actual variable value. This should be Str("blob", blob) instead of Str("blob", "blob").

Suggested change

d.log.Debug().Str("digest", digest.String()).Str("blob", "blob").Msg("checking blob in cache")

d.log.Debug().Str("digest", digest.String()).Str("blob", blob).Msg("checking blob in cache")

Copilot · 2025-11-23T20:50:41Z

 		So(err, ShouldBeNil)

-		So(blobs, ShouldResemble, []string{"second"})
+		//So(blobs, ShouldResemble, []string{"second"})


Commented out code should be removed. If the expected behavior has changed, remove the old assertion entirely rather than commenting it out.

Suggested change

//So(blobs, ShouldResemble, []string{"second"})

Copilot · 2025-11-23T20:50:42Z

+	// FIXME: also keep cache in sync
+	// FIXME: we don't have dedupe flag here!


FIXME comments indicate incomplete work. These should be addressed before merging or converted to TODO comments with tracking issue references.

Suggested change

// FIXME: also keep cache in sync

// FIXME: we don't have dedupe flag here!

// TODO: also keep cache in sync (see issue #1234)

// TODO: we don't have dedupe flag here! (see issue #1234)

Copilot · 2025-11-23T20:50:42Z


 		// cache record exists, but due to GC and upgrades from older versions,
 		// disk content and cache records may go out of sync
+		is.log.Debug().Bool("relpath?", is.cache.UsesRelativePaths()).Msg("check this")


Debug logging statement with hardcoded string "check this" should be removed or given a more meaningful message before merging.

Suggested change

is.log.Debug().Bool("relpath?", is.cache.UsesRelativePaths()).Msg("check this")

is.log.Debug().Bool("relpath?", is.cache.UsesRelativePaths()).Msg("checking if cache uses relative paths for dedupe")

Copilot · 2025-11-23T20:50:42Z

 		err = cacheDriver.DeleteBlob("key", "bogusValue")
-		So(err, ShouldBeNil)
+		So(err, ShouldEqual, errors.ErrCacheMiss)
+		//So(err, ShouldBeNil)


Commented out code should be removed. If this assertion is no longer valid, remove it entirely rather than commenting it out.

Suggested change

//So(err, ShouldBeNil)

Copilot · 2025-11-23T20:50:43Z


-		So(blobs, ShouldResemble, []string{"second", "third"})
+		So(blobs, ShouldResemble, []string{"first", "second", "third"})
+		//So(blobs, ShouldResemble, []string{"second", "third"})


Commented out code should be removed. If the expected behavior has changed, remove the old assertion entirely rather than commenting it out.

Suggested change

//So(blobs, ShouldResemble, []string{"second", "third"})

Copilot · 2025-11-23T20:50:43Z


 		err = cacheDriver.DeleteBlob("key", "bogusValue")
-		So(err, ShouldBeNil)
+		//So(err, ShouldBeNil)


Commented out code should be removed. If the expected behavior has changed, remove the old assertion entirely rather than commenting it out.

Suggested change

//So(err, ShouldBeNil)

Copilot · 2025-11-23T20:50:43Z

+	/*
+		if err := gc.cleanRepo(ctx, constants.GlobalBlobsRepo); err != nil {
+			errMessage := "failed to run GC for " + path.Join(gc.imgStore.RootDir(), constants.GlobalBlobsRepo)
+			gc.log.Error().Err(err).Str("module", "gc").Msg(errMessage)
+			gc.log.Info().Str("module", "gc").
+				Msg("gc unsuccessfully completed for " + path.Join(gc.imgStore.RootDir(), constants.GlobalBlobsRepo))
+
+			return err
+		}
+	*/
+


Large block of commented out code should be removed. If this logic is not needed yet, consider removing it or creating a TODO with a tracking issue instead of leaving commented code.

Suggested change

/*

if err := gc.cleanRepo(ctx, constants.GlobalBlobsRepo); err != nil {

errMessage := "failed to run GC for " + path.Join(gc.imgStore.RootDir(), constants.GlobalBlobsRepo)

gc.log.Error().Err(err).Str("module", "gc").Msg(errMessage)

gc.log.Info().Str("module", "gc").

Msg("gc unsuccessfully completed for " + path.Join(gc.imgStore.RootDir(), constants.GlobalBlobsRepo))

return err

}

*/

// TODO: Consider running cleanRepo for constants.GlobalBlobsRepo if/when needed. See issue tracker for details.

Copilot · 2025-11-23T20:50:43Z

+			// FIXME: this seems incorrect
+			return nil


FIXME comment with "this seems incorrect" indicates a known issue. This should be resolved before merging, as the code appears to be silently returning nil on validation errors.

Suggested change

// FIXME: this seems incorrect

return nil

// return the validation error so the caller is aware of the failure

return err

Currently, zot uses one of the repos as the master copy for a blob to achieve dedupe. However, blobs can be deleted from repos and this complicates dedupe tracking logic. Now use a single hidden global repo as a blob store instead. Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

github-actions · 2026-03-01T02:14:06Z

This PR is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 10 days.

github-actions · 2026-03-12T02:13:46Z

This PR was closed because it has been stalled for 10 days with no activity.

rchincha · 2026-03-28T21:36:09Z

superseded by #3906

rchincha force-pushed the fix-dedupe branch from 8bee9dc to f789a29 Compare August 19, 2025 07:45

rchincha force-pushed the fix-dedupe branch 5 times, most recently from 6edb9fb to b4c3c46 Compare September 4, 2025 05:23

andaaron reviewed Sep 4, 2025

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rchincha force-pushed the fix-dedupe branch 6 times, most recently from 4b2da37 to da2884a Compare September 11, 2025 05:24

rchincha force-pushed the fix-dedupe branch 3 times, most recently from 49521a6 to 23f1ebc Compare October 10, 2025 06:47

rchincha force-pushed the fix-dedupe branch from 23f1ebc to 3c6902e Compare October 16, 2025 06:46

andaaron reviewed Oct 20, 2025

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rchincha force-pushed the fix-dedupe branch from f628cfb to e283314 Compare November 23, 2025 08:11

rchincha requested a review from Copilot November 23, 2025 20:43

Copilot started reviewing on behalf of rchincha November 23, 2025 20:44 View session

Copilot finished reviewing on behalf of rchincha November 23, 2025 20:46

Copilot AI reviewed Nov 23, 2025

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rchincha added 6 commits November 25, 2025 23:26

fix: dedupe fix

f6ac2ae

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: fix dedupe

8f980ce

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: tests

6d75227

fix: test

555aa73

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: disable dedupe task generators

75ed494

rchincha added 11 commits November 25, 2025 23:26

fix: dedupe

100dc65

fix: dedupe

f4b47e4

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: add more debugs

17c104f

fix: fix cache logic

abe6bad

fix: dyanmodb cache logic

3de16d3

fix: test

9f3da79

fix: cache

8ac4e36

fix: some boltdb changes

1e2a597

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: botldb

db7153f

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

fix: botdb fixes

9129807

fix: test cases

b2bd4d2

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

rchincha force-pushed the fix-dedupe branch from e283314 to a04f1b9 Compare November 29, 2025 01:57

fix: dynamodb fixes

e4d2e9e

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

rchincha force-pushed the fix-dedupe branch from a04f1b9 to 3da7b4b Compare November 29, 2025 09:10

fix: add redis support

79ca683

Signed-off-by: Ramkumar Chinchani <rchincha.dev@gmail.com>

rchincha force-pushed the fix-dedupe branch from 3da7b4b to 79ca683 Compare November 30, 2025 06:11

github-actions Bot added the no-pr-activity label Mar 1, 2026

github-actions Bot closed this Mar 12, 2026

rchincha reopened this Mar 12, 2026

rchincha added awaiting-feedback and removed no-pr-activity labels Mar 12, 2026

rchincha closed this Mar 28, 2026

	// create nested deduped bucket where we store all the deduped blobs + original blob
	// create nested deduped bucket where we store all the deduped blobs while excluding the original blob

	d.log.Debug().Str("digest", digest.String()).Str("blob", "blob").Msg("checking blob in cache")
	d.log.Debug().Str("digest", digest.String()).Str("blob", blob).Msg("checking blob in cache")

		// FIXME: also keep cache in sync
		// FIXME: we don't have dedupe flag here!

	is.log.Debug().Bool("relpath?", is.cache.UsesRelativePaths()).Msg("check this")
	is.log.Debug().Bool("relpath?", is.cache.UsesRelativePaths()).Msg("checking if cache uses relative paths for dedupe")

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