fix(gc): sync repodb when gc'ing manifests (#1819)

fix(gc): fix cleaning deduped blobs because they have the modTime of
the original blobs, fixed by updating the modTime when hard linking
the blobs.
fix(gc): failing to parse rootDir at zot startup when using s3 storage
because there are no files under rootDir and we can not create empty dirs
on s3, fixed by creating an empty file under rootDir.

Signed-off-by: Petu Eusebiu <peusebiu@cisco.com>

pkg/api/controller_test.go

@@ -60,6 +60,7 @@ import (
 	"zotregistry.io/zot/pkg/meta"
 	"zotregistry.io/zot/pkg/storage"
 	storageConstants "zotregistry.io/zot/pkg/storage/constants"
+	"zotregistry.io/zot/pkg/storage/gc"
 	"zotregistry.io/zot/pkg/test"
 	testc "zotregistry.io/zot/pkg/test/common"
 	. "zotregistry.io/zot/pkg/test/image-utils"
@@ -2338,11 +2339,9 @@ func TestBearerAuthWrongAuthorizer(t *testing.T) {
 			},
 		}
 		ctlr := makeController(conf, t.TempDir())
-		cm := test.NewControllerManager(ctlr)
 
 		So(func() {
-			ctx := context.Background()
-			cm.RunServer(ctx)
+			api.AuthHandler(ctlr)
 		}, ShouldPanic)
 	})
 }
@@ -7665,7 +7664,7 @@ func TestInjectTooManyOpenFiles(t *testing.T) {
 	})
 }
 
-func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
+func TestGCSignaturesAndUntaggedManifestsWithMetaDB(t *testing.T) {
 	Convey("Make controller", t, func() {
 		Convey("Garbage collect signatures without subject and manifests without tags", func(c C) {
 			repoName := "testrepo" //nolint:goconst
@@ -7676,6 +7675,16 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 			conf := config.New()
 			conf.HTTP.Port = port
 
+			value := true
+			searchConfig := &extconf.SearchConfig{
+				BaseConfig: extconf.BaseConfig{Enable: &value},
+			}
+
+			// added search extensions so that metaDB is initialized and its tested in GC logic
+			conf.Extensions = &extconf.ExtensionConfig{
+				Search: searchConfig,
+			}
+
 			ctlr := makeController(conf, t.TempDir())
 
 			dir := t.TempDir()
@@ -7686,15 +7695,24 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 
 			ctlr.Config.Storage.Dedupe = false
 
-			err := test.WriteImageToFileSystem(CreateDefaultImage(), repoName, tag,
-				test.GetDefaultStoreController(dir, ctlr.Log))
-			So(err, ShouldBeNil)
-
 			cm := test.NewControllerManager(ctlr)
 			cm.StartServer()
 			cm.WaitServerToBeReady(port)
 			defer cm.StopServer()
 
+			img := CreateDefaultImage()
+
+			err := UploadImage(img, baseURL, repoName, tag)
+			So(err, ShouldBeNil)
+
+			gc := gc.NewGarbageCollect(ctlr.StoreController.DefaultStore, ctlr.MetaDB,
+				gc.Options{
+					Referrers:      ctlr.Config.Storage.GCReferrers,
+					Delay:          ctlr.Config.Storage.GCDelay,
+					RetentionDelay: ctlr.Config.Storage.UntaggedImageRetentionDelay,
+				},
+				ctlr.Log)
+
 			resp, err := resty.R().Get(baseURL + fmt.Sprintf("/v2/%s/manifests/%s", repoName, tag))
 			So(err, ShouldBeNil)
 			So(resp.StatusCode(), ShouldEqual, http.StatusOK)
@@ -7748,6 +7766,9 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 			So(err, ShouldBeNil)
 			So(resp.StatusCode(), ShouldEqual, http.StatusOK)
 
+			cosignDigest := resp.Header().Get(constants.DistContentDigestKey)
+			So(cosignDigest, ShouldNotBeEmpty)
+
 			// get notation signature manifest
 			resp, err = resty.R().SetQueryParam("artifactType", notreg.ArtifactTypeNotation).Get(
 				fmt.Sprintf("%s/v2/%s/referrers/%s", baseURL, repoName, digest.String()))
@@ -7760,6 +7781,20 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 			So(err, ShouldBeNil)
 			So(len(index.Manifests), ShouldEqual, 1)
 
+			// shouldn't do anything
+			err = gc.CleanRepo(repoName)
+			So(err, ShouldBeNil)
+
+			// make sure both signatures are stored in repodb
+			repoMeta, err := ctlr.MetaDB.GetRepoMeta(repoName)
+			So(err, ShouldBeNil)
+
+			sigMeta := repoMeta.Signatures[digest.String()]
+			So(len(sigMeta[storage.CosignType]), ShouldEqual, 1)
+			So(len(sigMeta[storage.NotationType]), ShouldEqual, 1)
+			So(sigMeta[storage.CosignType][0].SignatureManifestDigest, ShouldEqual, cosignDigest)
+			So(sigMeta[storage.NotationType][0].SignatureManifestDigest, ShouldEqual, index.Manifests[0].Digest.String())
+
 			Convey("Trigger gcNotationSignatures() error", func() {
 				var refs ispec.Index
 				err = json.Unmarshal(resp.Body(), &refs)
@@ -7773,7 +7808,7 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 				err = UploadImage(img, baseURL, repoName, img.DigestStr())
 				So(err, ShouldBeNil)
 
-				err = ctlr.StoreController.DefaultStore.RunGCRepo(repoName)
+				err = gc.CleanRepo(repoName)
 				So(err, ShouldNotBeNil)
 
 				err = os.Chmod(path.Join(dir, repoName, "blobs", "sha256", refs.Manifests[0].Digest.Encoded()), 0o755)
@@ -7787,7 +7822,7 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 				err = UploadImage(img, baseURL, repoName, tag)
 				So(err, ShouldBeNil)
 
-				err = ctlr.StoreController.DefaultStore.RunGCRepo(repoName)
+				err = gc.CleanRepo(repoName)
 				So(err, ShouldNotBeNil)
 
 				err = os.WriteFile(path.Join(dir, repoName, "blobs", "sha256", refs.Manifests[0].Digest.Encoded()), content, 0o600)
@@ -7811,6 +7846,17 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 					}, baseURL, repoName, untaggedManifestDigest.String())
 				So(err, ShouldBeNil)
 
+				// make sure repoDB reference was added
+				repoMeta, err := ctlr.MetaDB.GetRepoMeta(repoName)
+				So(err, ShouldBeNil)
+
+				_, ok := repoMeta.Referrers[untaggedManifestDigest.String()]
+				So(ok, ShouldBeTrue)
+				_, ok = repoMeta.Signatures[untaggedManifestDigest.String()]
+				So(ok, ShouldBeTrue)
+				_, ok = repoMeta.Statistics[untaggedManifestDigest.String()]
+				So(ok, ShouldBeTrue)
+
 				// overwrite image so that signatures will get invalidated and gc'ed
 				cfg, layers, manifest, err = test.GetImageComponents(3) //nolint:staticcheck
 				So(err, ShouldBeNil)
@@ -7827,9 +7873,24 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 				So(err, ShouldBeNil)
 				newManifestDigest := godigest.FromBytes(manifestBuf)
 
-				err = ctlr.StoreController.DefaultStore.RunGCRepo(repoName)
+				err = gc.CleanRepo(repoName)
 				So(err, ShouldBeNil)
 
+				// make sure both signatures are removed from repodb and repo reference for untagged is removed
+				repoMeta, err = ctlr.MetaDB.GetRepoMeta(repoName)
+				So(err, ShouldBeNil)
+
+				sigMeta := repoMeta.Signatures[digest.String()]
+				So(len(sigMeta[storage.CosignType]), ShouldEqual, 0)
+				So(len(sigMeta[storage.NotationType]), ShouldEqual, 0)
+
+				_, ok = repoMeta.Referrers[untaggedManifestDigest.String()]
+				So(ok, ShouldBeFalse)
+				_, ok = repoMeta.Signatures[untaggedManifestDigest.String()]
+				So(ok, ShouldBeFalse)
+				_, ok = repoMeta.Statistics[untaggedManifestDigest.String()]
+				So(ok, ShouldBeFalse)
+
 				// both signatures should be gc'ed
 				resp, err = resty.R().Get(baseURL + fmt.Sprintf("/v2/%s/manifests/%s", repoName, cosignTag))
 				So(err, ShouldBeNil)
@@ -7885,6 +7946,13 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 			cm.StartAndWait(port)
 			defer cm.StopServer()
 
+			gc := gc.NewGarbageCollect(ctlr.StoreController.DefaultStore, ctlr.MetaDB,
+				gc.Options{
+					Referrers:      ctlr.Config.Storage.GCReferrers,
+					Delay:          ctlr.Config.Storage.GCDelay,
+					RetentionDelay: ctlr.Config.Storage.UntaggedImageRetentionDelay,
+				}, ctlr.Log)
+
 			resp, err := resty.R().Get(baseURL + fmt.Sprintf("/v2/%s/manifests/%s", repoName, tag))
 			So(err, ShouldBeNil)
 			So(resp.StatusCode(), ShouldEqual, http.StatusOK)
@@ -7934,7 +8002,7 @@ func TestGCSignaturesAndUntaggedManifests(t *testing.T) {
 			So(err, ShouldBeNil)
 			So(resp.StatusCode(), ShouldEqual, http.StatusCreated)
 
-			err = ctlr.StoreController.DefaultStore.RunGCRepo(repoName)
+			err = gc.CleanRepo(repoName)
 			So(err, ShouldBeNil)
 
 			resp, err = resty.R().SetHeader("Content-Type", ispec.MediaTypeImageIndex).