SOF-7926: generic InMemoryEntity

dist/js/generated/MethodSchemaMixin.d.ts

@@ -1,5 +1,5 @@
 import type { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import type { BaseMethod } from "@mat3ra/esse/dist/js/types";
+import type { BaseInMemoryEntitySchema, BaseMethod } from "@mat3ra/esse/dist/js/types";
 export type MethodSchemaMixin = BaseMethod;
-export type MethodInMemoryEntity = InMemoryEntity & MethodSchemaMixin;
+export type MethodInMemoryEntity = InMemoryEntity<BaseInMemoryEntitySchema & MethodSchemaMixin>;
 export declare function methodSchemaMixin<T extends InMemoryEntity>(item: InMemoryEntity): asserts item is T & MethodSchemaMixin;

dist/js/generated/ModelSchemaMixin.d.ts

@@ -1,5 +1,5 @@
 import type { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import type { BaseModel } from "@mat3ra/esse/dist/js/types";
+import type { BaseInMemoryEntitySchema, BaseModel } from "@mat3ra/esse/dist/js/types";
 export type ModelSchemaMixin = BaseModel;
-export type ModelInMemoryEntity = InMemoryEntity & ModelSchemaMixin;
+export type ModelInMemoryEntity = InMemoryEntity<BaseInMemoryEntitySchema & ModelSchemaMixin>;
 export declare function modelSchemaMixin<T extends InMemoryEntity>(item: InMemoryEntity): asserts item is T & ModelSchemaMixin;

dist/js/method.d.ts

@@ -1,23 +1,24 @@
 import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
 import { type HashedEntity } from "@mat3ra/code/dist/js/entity/mixins/HashedEntityMixin";
-import type { Constructor } from "@mat3ra/code/dist/js/utils/types";
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
-import type { BaseMethod, SlugifiedEntry } from "@mat3ra/esse/dist/js/types";
+import type { BaseInMemoryEntitySchema, BaseMethod, FileDataItem, SlugifiedEntry } from "@mat3ra/esse/dist/js/types";
 import { type MethodSchemaMixin } from "./generated/MethodSchemaMixin";
-type Base = typeof InMemoryEntity & Constructor<MethodSchemaMixin> & Constructor<HashedEntity>;
+type MethodEntity = BaseMethod & BaseInMemoryEntitySchema;
+export interface Method extends MethodSchemaMixin, HashedEntity {
+}
 interface MethodData extends Record<string, unknown> {
     searchText?: string;
+    pseudo?: FileDataItem[];
+    allPseudo?: FileDataItem[];
 }
-declare const Method_base: Base;
-export declare class Method extends Method_base implements BaseMethod {
+export declare class Method extends InMemoryEntity<MethodEntity> implements BaseMethod, HashedEntity {
     constructor(config: BaseMethod);
-    toJSON: () => BaseMethod & AnyObject;
     cloneWithoutData(): Method;
     setSubtype(subtype: SlugifiedEntry): void;
     static get defaultConfig(): {
         readonly type: "pseudopotential";
         readonly subtype: "us";
     };
+    get methodData(): MethodData;
     get searchText(): string;
     setSearchText(searchText: string): void;
     setData(data?: MethodData): void;

dist/js/method.js

@@ -22,17 +22,22 @@ class Method extends entity_1.InMemoryEntity {
     static get defaultConfig() {
         return default_methods_1.PseudopotentialMethodConfig;
     }
+    get methodData() {
+        var _a;
+        return (_a = this.data) !== null && _a !== void 0 ? _a : {};
+    }
     get searchText() {
-        return this.prop("data.searchText", "");
+        var _a;
+        return (_a = this.methodData.searchText) !== null && _a !== void 0 ? _a : "";
     }
     setSearchText(searchText) {
-        this.setData({ ...this.data, searchText });
+        this.setData({ ...this.methodData, searchText });
     }
     setData(data = {}) {
-        this.setProp("data", data);
+        this.data = data;
     }
     cleanData(fieldsToExclude = []) {
-        const filteredData = { ...this.data };
+        const filteredData = { ...this.methodData };
         fieldsToExclude.forEach((field) => {
             delete filteredData[field];
         });

dist/js/methods/pseudopotential.d.ts

@@ -1,4 +1,3 @@
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
 import { type BaseMethod, type FileDataItem } from "@mat3ra/esse/dist/js/types";
 import { PseudopotentialFilter, PseudopotentialMetaProperty } from "@mat3ra/prode";
 import { Method } from "../method";
@@ -7,7 +6,6 @@ export type ExchangeCorrelation = {
     functional: string;
 };
 export declare class PseudopotentialMethod extends Method {
-    toJSON: () => BaseMethod & AnyObject;
     get pseudo(): FileDataItem[];
     get allPseudo(): FileDataItem[];
     get pseudopotentials(): PseudopotentialMetaProperty[];

dist/js/methods/pseudopotential.js

@@ -9,10 +9,12 @@ const underscore_1 = __importDefault(require("underscore"));
 const method_1 = require("../method");
 class PseudopotentialMethod extends method_1.Method {
     get pseudo() {
-        return this.prop("data.pseudo", []);
+        var _a;
+        return (_a = this.methodData.pseudo) !== null && _a !== void 0 ? _a : [];
     }
     get allPseudo() {
-        return this.prop("data.allPseudo", []);
+        var _a;
+        return (_a = this.methodData.allPseudo) !== null && _a !== void 0 ? _a : [];
     }
     get pseudopotentials() {
         return this.pseudo.map((config) => new prode_1.PseudopotentialMetaProperty(config));
@@ -37,13 +39,13 @@ class PseudopotentialMethod extends method_1.Method {
     }
     setPseudopotentials(pseudopotentials) {
         this.setData({
-            ...this.data,
+            ...this.methodData,
             pseudo: underscore_1.default.sortBy(pseudopotentials, "element").map((item) => item.toJSON()),
         });
     }
     setAllPseudopotentials(pseudopotentials) {
         this.setData({
-            ...this.data,
+            ...this.methodData,
             allPseudo: underscore_1.default.sortBy(pseudopotentials, "element").map((item) => item.toJSON()),
         });
     }

dist/js/model.d.ts

@@ -1,15 +1,20 @@
 import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
 import { type HashedEntity } from "@mat3ra/code/dist/js/entity/mixins/HashedEntityMixin";
-import type { Constructor } from "@mat3ra/code/dist/js/utils/types";
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
-import type { AnyModelSchema, ApplicationSchema, BaseMethod, BaseModel, SlugifiedEntry, SlugifiedEntryOrSlug } from "@mat3ra/esse/dist/js/types";
+import type { ApplicationSchema, BaseInMemoryEntitySchema, BaseMethod, BaseModel, SlugifiedEntry, SlugifiedEntryOrSlug } from "@mat3ra/esse/dist/js/types";
 import { type ModelSchemaMixin } from "./generated/ModelSchemaMixin";
 import { Method } from "./method";
 import { MethodFactory } from "./methods/factory";
 import type { MethodTreeBranch, ModelConfig, ModelTree } from "./types";
-type Base = typeof InMemoryEntity & Constructor<ModelSchemaMixin> & Constructor<HashedEntity>;
-declare const Model_base: Base;
-export declare class Model extends Model_base implements BaseModel {
+export type ModelEntity = BaseInMemoryEntitySchema & Pick<BaseModel, "method"> & {
+    type: string;
+    subtype: SlugifiedEntryOrSlug;
+    refiners?: SlugifiedEntry[];
+    modifiers?: SlugifiedEntry[];
+    functional?: string;
+};
+export interface Model extends ModelSchemaMixin, HashedEntity {
+}
+export declare class Model extends InMemoryEntity<ModelEntity> implements BaseModel {
     protected _application?: ApplicationSchema;
     protected _MethodFactory: typeof MethodFactory;
     protected _method?: Method;
@@ -39,11 +44,9 @@ export declare class Model extends Model_base implements BaseModel {
         subtype: "gga";
     };
     static get allTypes(): SlugifiedEntry[];
-    _json: AnyModelSchema & AnyObject;
-    toJSON(): AnyModelSchema & AnyObject;
+    toJSON(): ModelEntity;
     protected _stringToSlugifiedObject(slug: SlugifiedEntryOrSlug): SlugifiedEntry;
     get isUnknown(): boolean;
     protected get subtypeSlug(): string;
     getHashObject(): Record<string, unknown>;
 }
-export {};

dist/js/model.js

@@ -16,7 +16,7 @@ const EMPTY_BRANCH = { methods: {} };
 class Model extends entity_1.InMemoryEntity {
     constructor(config) {
         const { application, method = method_1.Method.defaultConfig, ...entityConfig } = config;
-        super(entityConfig);
+        super({ ...entityConfig, method });
         this._application = application;
         this._MethodFactory = factory_1.MethodFactory;
         this.method = method || this.method;

dist/js/models/dft.d.ts

@@ -14,16 +14,15 @@ export declare class DFTModel extends Model {
     readonly defaultRefiners: SlugifiedEntry[];
     readonly defaultModifiers: SlugifiedEntry[];
     get slugifiedFunctional(): SlugifiedEntry;
-    get functional(): "pz" | "pw" | "vwn" | "other" | "pbe" | "pbesol" | "pw91" | "b3lyp" | "hse06";
-    set functional(functional: "pz" | "pw" | "vwn" | "other" | "pbe" | "pbesol" | "pw91" | "b3lyp" | "hse06");
-    get refiners(): SlugifiedEntry[];
-    get modifiers(): SlugifiedEntry[];
+    get functional(): string | undefined;
+    set functional(functional: string | undefined);
+    get refiners(): SlugifiedEntry[] | undefined;
+    get modifiers(): SlugifiedEntry[] | undefined;
     setSubtype(subtype: SlugifiedEntryOrSlug): void;
     setFunctional(functional: string): void;
     private _setArrayProp;
     setRefiners(refiners: SlugifiedEntryOrSlug | SlugifiedEntryOrSlug[]): void;
     setModifiers(modifiers: SlugifiedEntryOrSlug | SlugifiedEntryOrSlug[]): void;
-    _json: DFTModelSchema & AnyObject;
     toJSON(): DFTModelSchema & AnyObject;
     get allFunctionals(): SlugifiedEntry[];
     get allRefiners(): SlugifiedEntry[];

dist/js/models/dft.js

@@ -11,15 +11,14 @@ class DFTModel extends model_1.Model {
         this.defaultRefiners = [];
         this.defaultModifiers = [];
         this._MethodFactory = config.MethodFactory || factory_1.MethodFactory;
-        this.functional =
-            this.prop("functional") || this.defaultFunctional.slug;
+        this.functional = this.prop("functional") || this.defaultFunctional.slug;
     }
     get groupSlug() {
-        var _a;
-        const refinersSlug = this.refiners.map((o) => o.slug).join("+");
-        const modifiersSlug = this.modifiers.map((o) => o.slug).join("+");
+        var _a, _b, _c;
+        const refinersSlug = ((_a = this.refiners) !== null && _a !== void 0 ? _a : []).map((o) => o.slug).join("+");
+        const modifiersSlug = ((_b = this.modifiers) !== null && _b !== void 0 ? _b : []).map((o) => o.slug).join("+");
         const slugs = [
-            (_a = this._application) === null || _a === void 0 ? void 0 : _a.shortName,
+            (_c = this._application) === null || _c === void 0 ? void 0 : _c.shortName,
             this.type,
             this.subtype,
             this.functional,
@@ -33,7 +32,8 @@ class DFTModel extends model_1.Model {
         return (0, tree_1.treeSlugToNamedObject)(slug);
     }
     get slugifiedFunctional() {
-        return this._stringToSlugifiedObject(this.functional);
+        var _a;
+        return this._stringToSlugifiedObject((_a = this.functional) !== null && _a !== void 0 ? _a : this.defaultFunctional.slug);
     }
     get functional() {
         return this.requiredProp("functional");