Switch ResourceManager update cache to JSON Patch (#442)

It was previously using JSON Merge Patch, which will recreate structures
that are trying to be deleted. JSON Patch will fail to apply the patch
if the structure being patched doesn't exist.

For example, if a reconciler defined a volume on a Deployment on
create/update a mutating webhook will default the file permissions. If
the reconciler later needs to remove that volume, the defaulted file
permissions will no longer be re-applied.

Signed-off-by: Scott Andrews <andrewssc@vmware.com>

reconcilers/resourcemanager.go

@@ -13,9 +13,10 @@ import (
 	"sync"
 	"time"
 
-	jsonpatch "github.com/evanphx/json-patch/v5"
+	jsonmergepatch "github.com/evanphx/json-patch/v5"
 	"github.com/go-logr/logr"
 	"github.com/google/go-cmp/cmp"
+	jsonpatch "gomodules.xyz/jsonpatch/v2"
 	corev1 "k8s.io/api/core/v1"
 	"k8s.io/apimachinery/pkg/api/equality"
 	"k8s.io/apimachinery/pkg/util/cache"
@@ -184,8 +185,8 @@ func (r *ResourceManager[T]) Manage(ctx context.Context, resource client.Object,
 		// the only object added to the cache is *Patch
 		err := patch.(*Patch).Apply(desiredPatched)
 		if err != nil {
-			// there's not much we can do, but let the normal update proceed
-			log.Info("unable to patch desired child from mutation cache")
+			// there's not much we can do, let the normal update proceed
+			log.Info("unable to patch desired child from mutation cache, this error is usually benign", "error", err.Error())
 		}
 	}
 
@@ -218,7 +219,7 @@ func (r *ResourceManager[T]) Manage(ctx context.Context, resource client.Object,
 	patch, err := NewPatch(base, current)
 	if err != nil {
 		if !errors.Is(err, ErrQuiet) {
-			log.Error(err, "unable to generate mutation patch", "snapshot", r.sanitize(desired), "base", r.sanitize(base))
+			log.Info("unable to generate mutation patch", "snapshot", r.sanitize(desired), "base", r.sanitize(base), "error", err.Error())
 		}
 	} else {
 		r.mutationCache.Set(current.GetUID(), patch, 1*time.Hour)
@@ -253,14 +254,18 @@ func NewPatch(base, update client.Object) (*Patch, error) {
 	if err != nil {
 		return nil, err
 	}
-	patch, err := jsonpatch.CreateMergePatch(baseBytes, updateBytes)
+	patch, err := jsonpatch.CreatePatch(baseBytes, updateBytes)
+	if err != nil {
+		return nil, err
+	}
+	patchBytes, err := json.Marshal(patch)
 	if err != nil {
 		return nil, err
 	}
 
 	return &Patch{
 		generation: base.GetGeneration(),
-		bytes:      patch,
+		bytes:      patchBytes,
 	}, nil
 }
 
@@ -280,7 +285,11 @@ func (p *Patch) Apply(rebase client.Object) error {
 	if err != nil {
 		return err
 	}
-	patchedBytes, err := jsonpatch.MergePatch(rebaseBytes, p.bytes)
+	merge, err := jsonmergepatch.DecodePatch(p.bytes)
+	if err != nil {
+		return err
+	}
+	patchedBytes, err := merge.Apply(rebaseBytes)
 	if err != nil {
 		return err
 	}