Merge pull request #84 from axelboc/fix-datatype

Fix calling `get_attribute_names` on committed datatype

.editorconfig

@@ -0,0 +1,9 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 2
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 ## v0.7.8 TBC
+### Fixed
+- Fix accessing attributes of committed datatype with `my_datafile.attrs`.
+- Fix calling `get_attribute_names` method of Module API on committed datatype.
 ### Changed
 - Mark optional parameters as such in the TypeScript declarations of the following `H5Module` methods: `open`, `create_dataset`, `create_group`, `create_vlen_str_dataset` and `get_keys_vector`.
 ## v0.7.7 2024-08-28

src/hdf5_hl.d.ts

@@ -39,6 +39,7 @@ declare enum OBJECT_TYPE {
     REFERENCE = "Reference",
     REGION_REFERENCE = "RegionReference"
 }
+export declare type Entity = Dataset | Group | BrokenSoftLink | ExternalLink | Datatype | Reference | RegionReference;
 export declare class BrokenSoftLink {
     target: string;
     type: OBJECT_TYPE;
@@ -50,13 +51,6 @@ export declare class ExternalLink {
     type: OBJECT_TYPE;
     constructor(filename: string, obj_path: string);
 }
-export declare class Datatype {
-    file_id: bigint;
-    path: string;
-    type: OBJECT_TYPE;
-    constructor(file_id: bigint, path: string);
-    get metadata(): Metadata;
-}
 export declare class Reference {
     ref_data: Uint8Array;
     constructor(ref_data: Uint8Array);
@@ -81,30 +75,33 @@ declare abstract class HasAttrs {
     file_id: bigint;
     path: string;
     type: OBJECT_TYPE;
-    get attrs(): {
-        [key: string]: Attribute;
-    };
+    get attrs(): Record<string, Attribute>;
     get root(): Group;
     get parent(): Group;
     get_attribute(name: string, json_compatible: true): JSONCompatibleOutputData;
     get_attribute(name: string, json_compatible: false): OutputData;
     create_attribute(name: string, data: GuessableDataTypes, shape?: number[] | null, dtype?: string | null): void;
     delete_attribute(name: string): number;
     create_reference(): Reference;
-    dereference(ref: Reference | RegionReference): BrokenSoftLink | ExternalLink | Datatype | Group | Dataset | DatasetRegion | null;
+    dereference(ref: RegionReference): DatasetRegion;
+    dereference(ref: Reference | RegionReference): DatasetRegion | Entity | null;
+}
+export declare class Datatype extends HasAttrs {
+    constructor(file_id: bigint, path: string);
+    get metadata(): Metadata;
 }
 export declare class Group extends HasAttrs {
     constructor(file_id: bigint, path: string);
-    keys(): Array<string>;
-    values(): Generator<BrokenSoftLink | ExternalLink | Datatype | Group | Dataset | null, void, unknown>;
-    items(): Generator<(string | BrokenSoftLink | ExternalLink | Datatype | Group | Dataset | null)[], void, unknown>;
+    keys(): string[];
+    values(): Generator<Entity | null, void, never>;
+    items(): Generator<[string, Entity | null], void, never>;
     get_type(obj_path: string): number;
     get_link(obj_path: string): string;
     get_external_link(obj_path: string): {
         filename: string;
         obj_path: string;
     };
-    get(obj_name: string): BrokenSoftLink | ExternalLink | Datatype | Group | Dataset | null;
+    get(obj_name: string): Entity | null;
     create_group(name: string, track_order?: boolean): Group;
     create_dataset(args: {
         name: string;

src/hdf5_hl.ts

@@ -504,6 +504,8 @@ enum OBJECT_TYPE {
   REGION_REFERENCE = 'RegionReference',
 }
 
+export type Entity = Dataset | Group | BrokenSoftLink | ExternalLink | Datatype | Reference | RegionReference;
+
 export class BrokenSoftLink {
   // only used for broken links...
   target: string;
@@ -523,20 +525,6 @@ export class ExternalLink {
   }
 }
 
-export class Datatype {
-  file_id: bigint;
-  path: string;
-  type: OBJECT_TYPE = OBJECT_TYPE.DATATYPE
-  constructor(file_id: bigint, path: string) {
-    this.file_id = file_id;
-    this.path = path;
-  }
-
-  get metadata() {
-    return Module.get_datatype_metadata(this.file_id, this.path);
-  }
-}
-
 export class Reference {
   ref_data: Uint8Array;
   constructor(ref_data: Uint8Array) {
@@ -598,7 +586,7 @@ abstract class HasAttrs {
 
   get attrs() {
     let attr_names = Module.get_attribute_names(this.file_id, this.path) as string[];
-    let attrs: {[key: string]: Attribute}  = {};
+    let attrs: Record<string, Attribute>  = {};
     const { file_id, path } = this;
     for (let name of attr_names) {
       Object.defineProperty(attrs, name, {
@@ -607,7 +595,6 @@ abstract class HasAttrs {
       });
     }
     return attrs;
-
   }
 
   get root() {
@@ -677,14 +664,29 @@ abstract class HasAttrs {
     return new Reference(ref_data);
   }
 
-  dereference(ref: Reference | RegionReference) {
+  dereference(ref: RegionReference): DatasetRegion;
+  dereference(ref: Reference | RegionReference): DatasetRegion | Entity | null;
+  dereference(ref: Reference | RegionReference): DatasetRegion | Entity | null {
     const is_region = (ref instanceof RegionReference);
     const name = Module.get_referenced_name(this.file_id, ref.ref_data, !is_region);
     const target = this.root.get(name);
     return (is_region) ? new DatasetRegion(target as Dataset, ref) : target;
   }
 }
 
+export class Datatype extends HasAttrs {
+  constructor(file_id: bigint, path: string) {
+    super();
+    this.file_id = file_id;
+    this.path = path;
+    this.type = OBJECT_TYPE.DATATYPE;
+  }
+
+  get metadata() {
+    return Module.get_datatype_metadata(this.file_id, this.path);
+  }
+}
+
 export class Group extends HasAttrs {
   constructor(file_id: bigint, path: string) {
     super();
@@ -693,22 +695,22 @@ export class Group extends HasAttrs {
     this.type = OBJECT_TYPE.GROUP;
   }
 
-  keys(): Array<string> {
-    return Module.get_names(this.file_id, this.path, false) as string[];
+  keys(): string[] {
+    return Module.get_names(this.file_id, this.path, false);
   }
 
-  * values() {
+  * values(): Generator<Entity | null, void, never> {
     for (let name of this.keys()) {
       yield this.get(name);
     }
-    return
+    return;
   }
 
-  * items() {
+  * items(): Generator<[string, Entity | null], void, never> {
     for (let name of this.keys()) {
       yield [name, this.get(name)];
     }
-    return
+    return;
   }
 
   get_type(obj_path: string) {
@@ -723,7 +725,7 @@ export class Group extends HasAttrs {
     return Module.get_external_link(this.file_id, obj_path);
   }
 
-  get(obj_name: string) {
+  get(obj_name: string): Entity | null {
     let fullpath = (/^\//.test(obj_name)) ? obj_name : this.path + "/" + obj_name;
     fullpath = normalizePath(fullpath);
 

src/hdf5_util.cc

@@ -246,6 +246,10 @@ val get_attribute_names(hid_t loc_id, const std::string& obj_name_string)
     {
         ocpl_id = H5Gget_create_plist(obj_id);
     }
+    else if (obj_type == H5O_TYPE_NAMED_DATATYPE)
+    {
+        ocpl_id = H5Tget_create_plist(obj_id);
+    }
     else
     {
         ocpl_id = H5Dget_create_plist(obj_id);

test/datatype_test.mjs

@@ -18,6 +18,10 @@ async function datatype_test() {
     littleEndian: false,
     size: 10
   });
+
+  assert.deepEqual(Object.keys(datatype.attrs), ['named_dtype_attr']);
+  assert.deepEqual(datatype.attrs['named_dtype_attr'].value,
+    'An attribute of a named datatype');
 }
 
 export const tests = [

test/make_test_files.py

@@ -17,6 +17,7 @@
     f.create_dataset("bool", data=[[False, True], [True, False]], shape=(2,2))
     f.create_dataset("bigint", data=np.arange(8).reshape(2,2,2), dtype="<i8", shape=(2,2,2))
     f["datatype/value"] = np.dtype("S10")
+    f["datatype/value"].attrs["named_dtype_attr"] = "An attribute of a named datatype"
 
     f.create_dataset("bigendian", data=[3,2,1], dtype='>f4')
     f['bigendian'].attrs.create("bigendian_attr", [3,2,1], dtype='>i8')