Add support for storage transformers.

Author: zoj613

lib/extensions.ml

@@ -187,3 +187,88 @@ module Datatype = struct
     | `String "nativeint" -> Ok Nativeint
     | _ -> Error ("Unsupported metadata data_type")
 end
+
+type tf_error =
+  [ `Store_read of string
+  | `Store_write of string ]
+
+module type STF = sig
+  type t
+  val get : t -> string -> (string, [> tf_error]) result
+  val set : t -> string -> string -> unit
+  val erase : t -> string -> unit
+end
+
+module StorageTransformers = struct
+  type transformer =
+    | Identity
+  type t = transformer list
+
+  let default = [Identity]
+
+  let deserialize x =
+    match
+      Util.get_name x,
+      Yojson.Safe.Util.(member "configuration" x)
+    with
+    | "identity", `Null -> Ok Identity
+    | _ ->
+      Error "Unsupported storage transformer name or configuration."
+
+  let of_yojson x =
+    let open Util.Result_syntax in
+    List.fold_right
+      (fun x acc ->
+        acc >>= fun l ->
+        deserialize x >>| fun s ->
+        s :: l)  (Yojson.Safe.Util.to_list x) (Ok [])
+
+  let to_yojson x =
+    `List
+      (List.fold_right
+        (fun x acc ->
+          match x with
+          | Identity -> acc) x [])
+
+  let get
+    (type a)
+    (module M : STF with type t = a)
+    (store : a)
+    (transformers : t)
+    (key : string)
+    =
+    let open Util.Result_syntax in
+    M.get store key >>| fun raw ->
+    snd @@
+    List.fold_right
+      (fun x (k, v) ->
+        match x with
+        | Identity -> (k, v)) transformers (key, raw)
+
+  let set
+    (type a)
+    (module M : STF with type t = a)
+    (store : a)
+    (transformers : t)
+    (key : string)
+    (value : string)
+    =
+    let k', v' =
+      List.fold_left
+        (fun (k, v) -> function
+          | Identity -> (k, v)) (key, value) transformers
+    in
+    M.set store k' v'
+
+  let erase
+    (type a)
+    (module M : STF with type t = a)
+    (store : a)
+    (transformers : t)
+    (key : string)
+    =
+    M.erase store @@
+      List.fold_left
+        (fun k -> function
+          | Identity -> k) key transformers
+end

lib/extensions.mli

@@ -46,3 +46,30 @@ module Datatype : sig
   val of_yojson : Yojson.Safe.t -> (t, string) result
   val to_yojson : t -> Yojson.Safe.t
 end
+
+type tf_error =
+  [ `Store_read of string
+  | `Store_write of string ]
+
+module type STF = sig
+  type t
+  val get : t -> string -> (string, [> tf_error]) result
+  val set : t -> string -> string -> unit
+  val erase : t -> string -> unit
+end
+
+module StorageTransformers : sig
+  type transformer =
+    | Identity
+  type t = transformer list
+
+  val default : t
+  val get :
+    (module STF with type t = 'a) -> 'a -> t -> string -> (string, [> tf_error ]) result
+  val set :
+    (module STF with type t = 'a) -> 'a -> t -> string -> string -> unit
+  val erase :
+    (module STF with type t = 'a) -> 'a -> t -> string -> unit
+  val to_yojson : t -> Yojson.Safe.t
+  val of_yojson : Yojson.Safe.t -> (t, string) result
+end

lib/metadata.ml

@@ -112,13 +112,14 @@ module ArrayMetadata = struct
     ;chunk_key_encoding : ChunkKeyEncoding.t
     ;attributes : Yojson.Safe.t
     ;dimension_names : string option list
-    ;storage_transformers : Yojson.Safe.t Util.ExtPoint.t list}
+    ;storage_transformers : StorageTransformers.t}
 
   let create
     ?(sep=`Slash)
     ?(codecs=Codecs.Chain.default)
     ?(dimension_names=[])
     ?(attributes=`Null)
+    ?(storage_transformers=[])
     ~shape
     kind
     fv
@@ -134,7 +135,7 @@ module ArrayMetadata = struct
     ;dimension_names
     ;zarr_format = 3
     ;node_type = "array"
-    ;storage_transformers = []
+    ;storage_transformers
     ;fill_value = FillValue.of_kind kind fv
     ;data_type = Datatype.of_kind kind
     ;chunk_key_encoding = ChunkKeyEncoding.create sep}
@@ -168,6 +169,12 @@ module ArrayMetadata = struct
             | None -> `Null) xs
         in
         l @ [("dimension_names", `List xs')]
+    in
+    let l =
+      match t.storage_transformers with
+      | [] | [StorageTransformers.Identity] -> l
+      | xs ->
+        l @ [("storage_transformers", StorageTransformers.to_yojson xs)]
     in `Assoc l
 
   let of_yojson x =
@@ -256,8 +263,9 @@ module ArrayMetadata = struct
     >>= fun dimension_names ->
 
     (match member "storage_transformers" x with
-    | `Null -> Ok []
-    | _ -> Error "storage_transformers field is not yet supported.")
+    | `Null | `List [] -> Ok []
+    | _ ->
+      Error "storage_transformers field is not yet supported.")
     >>| fun storage_transformers ->
 
     {zarr_format; shape; node_type; data_type; codecs; fill_value; chunk_grid
@@ -286,6 +294,8 @@ module ArrayMetadata = struct
 
   let attributes t = t.attributes
 
+  let storage_transformers t = t.storage_transformers
+
   let chunk_shape t =
     RegularGrid.chunk_shape t.chunk_grid
 

lib/metadata.mli

@@ -38,6 +38,7 @@ module ArrayMetadata : sig
     ?codecs:Codecs.Chain.t ->
     ?dimension_names:string option list ->
     ?attributes:Yojson.Safe.t ->
+    ?storage_transformers:Extensions.StorageTransformers.t ->
     shape:int array ->
     ('a, 'b) Bigarray.kind ->
     'a ->
@@ -76,6 +77,10 @@ module ArrayMetadata : sig
   (** [attributes t] Returns a Yojson type containing user attributes assigned
       to the zarr array represented by [t]. *)
 
+  val storage_transformers : t -> Extensions.StorageTransformers.t
+  (** [storage_transformers t] Returns the storage transformers to be applied
+      to the keys and values of this store. *)
+
   val dimension_names : t -> string option list
   (** [dimension_name t] returns a list of dimension names. If none are
       defined then an empty list is returned. *)

lib/storage/storage.ml

@@ -8,6 +8,7 @@ module ArraySet = Util.ArraySet
 module Arraytbl = Util.Arraytbl
 module AM = Metadata.ArrayMetadata
 module GM = Metadata.GroupMetadata
+module ST = Extensions.StorageTransformers
 
 module Make (M : STORE) : S with type t = M.t = struct
   include M
@@ -35,6 +36,7 @@ module Make (M : STORE) : S with type t = M.t = struct
     ?(sep=`Slash)
     ?(dimension_names=[])
     ?(attributes=`Null)
+    ?(storage_transformers=[])
     ?codecs
     ~shape
     ~chunks
@@ -54,6 +56,7 @@ module Make (M : STORE) : S with type t = M.t = struct
       ~codecs
       ~dimension_names
       ~attributes
+      ~storage_transformers
       ~shape
       kind
       fill_value
@@ -154,11 +157,12 @@ module Make (M : STORE) : S with type t = M.t = struct
     in
     let codecs = AM.codecs meta in
     let prefix = ArrayNode.to_key node ^ "/" in
+    let tf = AM.storage_transformers meta in
     let cindices = ArraySet.of_seq @@ Arraytbl.to_seq_keys tbl in
     ArraySet.fold (fun idx acc ->
       acc >>= fun () ->
       let chunkkey = prefix ^ AM.chunk_key meta idx in
-      (match get t chunkkey with
+      (match ST.get (module M) t tf chunkkey with
       | Ok b ->
         Codecs.Chain.decode codecs repr b
       | Error _ ->
@@ -173,7 +177,7 @@ module Make (M : STORE) : S with type t = M.t = struct
       List.iter
         (fun (c, v) -> Ndarray.set arr c v) @@ Arraytbl.find_all tbl idx;
       Codecs.Chain.encode codecs arr >>| fun encoded ->
-      set t chunkkey encoded) cindices (Ok ())
+      ST.set (module M) t tf chunkkey encoded) cindices (Ok ())
 
   let get_array
   : type a b.
@@ -206,6 +210,7 @@ module Make (M : STORE) : S with type t = M.t = struct
     let tbl = Arraytbl.create @@ Array.length pair in
     let prefix = ArrayNode.to_key node ^ "/" in
     let chain = AM.codecs meta in
+    let tf = AM.storage_transformers meta in
     let repr =
       {kind
       ;shape = AM.chunk_shape meta
@@ -217,7 +222,7 @@ module Make (M : STORE) : S with type t = M.t = struct
       | Some arr ->
         Ok (Ndarray.get arr coord :: l)
       | None ->
-        (match get t @@ prefix ^ AM.chunk_key meta idx with
+        (match ST.get (module M) t tf @@ prefix ^ AM.chunk_key meta idx with
         | Ok b ->
           Codecs.Chain.decode chain repr b
         | Error _ ->
@@ -243,8 +248,9 @@ module Make (M : STORE) : S with type t = M.t = struct
       ArraySet.of_list @@ AM.chunk_indices meta @@ AM.shape meta in
     let s' =
       ArraySet.of_list @@ AM.chunk_indices meta shape in
+    let tf = AM.storage_transformers meta in
     ArraySet.iter
-      (fun v -> erase t @@ pre ^ AM.chunk_key meta v)
+      (fun v -> ST.erase (module M) t tf @@ pre ^ AM.chunk_key meta v)
       ArraySet.(diff s s');
     Ok (set t mkey @@ AM.encode @@ AM.update_shape meta shape)
 end

lib/storage/storage_intf.ml

@@ -56,6 +56,7 @@ module type S = sig
     : ?sep:[< `Dot | `Slash > `Slash ] ->
       ?dimension_names:string option list ->
       ?attributes:Yojson.Safe.t ->
+      ?storage_transformers:Extensions.StorageTransformers.t ->
       ?codecs:Codecs.chain ->
       shape:int array ->
       chunks:int array ->

lib/util.ml

@@ -1,13 +1,3 @@
-module ExtPoint = struct
-  type 'a t =
-    {name : string
-    ;configuration : 'a}
-
-  let ( = ) cmp x y =
-    (x.name = y.name) &&
-    cmp x.configuration y.configuration
-end
-
 type ('a, 'b) array_repr =
   {kind : ('a, 'b) Bigarray.kind
   ;shape : int array

lib/util.mli

@@ -5,13 +5,6 @@ type ('a, 'b) array_repr =
 (** The type summarizing the decoded/encoded representation of a Zarr array
     or chunk. *)
 
-module ExtPoint : sig
-  (** The type representing a JSON extension point metadata configuration. *)
-
-  type 'a t = {name : string ; configuration : 'a}
-  val ( = ) : ('a -> 'a -> bool) -> 'a t -> 'a t -> bool
-end
-
 module StrMap : sig include Hashtbl.S with type key = string end
 (** A hashtable with string keys. *)
 

lib/zarr.ml

@@ -5,3 +5,4 @@ module ArrayMetadata = Metadata.ArrayMetadata
 module GroupMetadata = Metadata.GroupMetadata
 module Storage = Storage
 module Codecs = Codecs
+module StorageTransformers = Extensions.StorageTransformers

lib/zarr.mli

@@ -5,3 +5,4 @@ module ArrayMetadata = Metadata.ArrayMetadata
 module GroupMetadata = Metadata.GroupMetadata
 module Storage = Storage
 module Codecs = Codecs
+module StorageTransformers = Extensions.StorageTransformers