SOF-7926: generic InMemoryEntity

dist/js/basis/basis.d.ts

@@ -1,5 +1,5 @@
 import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import { BasisSchema, Coordinate3DSchema, Vector3DSchema } from "@mat3ra/esse/dist/js/types";
+import { BaseInMemoryEntitySchema, BasisSchema, Coordinate3DSchema, Vector3DSchema } from "@mat3ra/esse/dist/js/types";
 import { Cell } from "../cell/cell";
 import { AtomicCoordinateValue, Coordinates } from "./coordinates";
 import { AtomicElementValue, Elements } from "./elements";
@@ -30,7 +30,8 @@ export interface ElementsAndCoordinatesConfig {
     units?: BasisSchema["units"];
     cell?: Cell;
 }
-export declare class Basis extends InMemoryEntity implements BasisSchema {
+type BasisEntitySchema = BasisConfig & BaseInMemoryEntitySchema;
+export declare class Basis extends InMemoryEntity<BasisEntitySchema> implements BasisSchema {
     static defaultConfig: BasisSchema;
     units: BasisSchema["units"];
     cell: Cell;
@@ -46,17 +47,17 @@ export declare class Basis extends InMemoryEntity implements BasisSchema {
     set coordinates(coordinates: BasisSchema["coordinates"]);
     get labels(): BasisSchema["labels"];
     set labels(labels: BasisSchema["labels"]);
-    toJSON(exclude?: string[]): BasisSchema;
-    clone(): Basis;
+    toJSON(exclude?: (keyof BasisConfig)[]): BasisSchema;
+    clone(): this;
     removeAllAtoms(): void;
     get cellRounded(): import("@mat3ra/esse/dist/js/types").Matrix3X3Schema;
     get elementsArray(): object[];
     getElementsAsObject(): BasisSchema["elements"];
     get coordinatesAsArray(): Coordinate3DSchema[];
     get isInCartesianUnits(): boolean;
     get isInCrystalUnits(): boolean;
-    toCartesian(): void;
-    toCrystal(): void;
+    toCartesian(): this;
+    toCrystal(): this;
     getElementByIndex(idx: number): AtomicElementValue;
     getElementById(id: number): AtomicElementValue;
     getCoordinateValueByIndex(idx: number): AtomicCoordinateValue;

dist/js/basis/basis.js

@@ -84,8 +84,6 @@ class Basis extends entity_1.InMemoryEntity {
     set labels(labels) {
         this._labels = labels_1.Labels.fromObjects(labels || []);
     }
-    // TODO: figure out how to override toJSON in the parent class with generic classes
-    // @ts-ignore
     toJSON(exclude = ["cell"]) {
         var _a;
         return {
@@ -96,7 +94,6 @@ class Basis extends entity_1.InMemoryEntity {
             ...(((_a = this.labels) === null || _a === void 0 ? void 0 : _a.length) ? { labels: this.labels } : {}),
         };
     }
-    // @ts-ignore
     clone() {
         const instance = super.clone();
         instance.cell = this.cell.clone();
@@ -127,15 +124,17 @@ class Basis extends entity_1.InMemoryEntity {
     }
     toCartesian() {
         if (this.isInCartesianUnits)
-            return;
+            return this;
         this._coordinates.mapArrayInPlace((point) => this.cell.convertPointToCartesian(point));
         this.units = constants_1.ATOMIC_COORD_UNITS.cartesian;
+        return this;
     }
     toCrystal() {
         if (this.isInCrystalUnits)
-            return;
+            return this;
         this._coordinates.mapArrayInPlace((point) => this.cell.convertPointToCrystal(point));
         this.units = constants_1.ATOMIC_COORD_UNITS.crystal;
+        return this;
     }
     getElementByIndex(idx) {
         return this._elements.getElementValueByIndex(idx);

dist/js/basis/constrained_basis.d.ts

@@ -15,7 +15,7 @@ export interface ElementsCoordinatesAndConstraintsConfig extends ElementsAndCoor
  * @extends Basis
  */
 export declare class ConstrainedBasis extends Basis {
-    _constraints: AtomicConstraints;
+    private _constraints;
     constructor(config: ConstrainedBasisConfig);
     static fromElementsCoordinatesAndConstraints(config: ElementsCoordinatesAndConstraintsConfig): ConstrainedBasis;
     get constraints(): AtomicConstraintsSchema;

dist/js/basis/constrained_basis.js

@@ -12,8 +12,7 @@ const helpers_1 = require("./helpers");
 class ConstrainedBasis extends basis_1.Basis {
     constructor(config) {
         super(config);
-        const { constraints } = config;
-        this._constraints = constraints_1.AtomicConstraints.fromObjects(constraints || []); // `constraints` is an Array with ids
+        this._constraints = constraints_1.AtomicConstraints.fromObjects(config.constraints); // `constraints` is an Array with ids
     }
     static fromElementsCoordinatesAndConstraints(config) {
         const basisConfig = this._convertValuesToConfig(config);

dist/js/generated/MaterialSchemaMixin.d.ts

@@ -0,0 +1,5 @@
+import type { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
+import type { MaterialPropertiesSchema } from "@mat3ra/esse/dist/js/types";
+export type MaterialSchemaMixin = MaterialPropertiesSchema;
+export type MaterialInMemoryEntity = InMemoryEntity & MaterialSchemaMixin;
+export declare function materialSchemaMixin<T extends InMemoryEntity>(item: InMemoryEntity): asserts item is T & MaterialSchemaMixin;

dist/js/generated/MaterialSchemaMixin.js

@@ -0,0 +1,76 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.materialSchemaMixin = void 0;
+function materialSchemaMixin(item) {
+    // @ts-expect-error
+    const properties = {
+        get formula() {
+            return this.prop("formula");
+        },
+        set formula(value) {
+            this.setProp("formula", value);
+        },
+        get unitCellFormula() {
+            return this.prop("unitCellFormula");
+        },
+        set unitCellFormula(value) {
+            this.setProp("unitCellFormula", value);
+        },
+        get basis() {
+            return this.requiredProp("basis");
+        },
+        set basis(value) {
+            this.setProp("basis", value);
+        },
+        get lattice() {
+            return this.requiredProp("lattice");
+        },
+        set lattice(value) {
+            this.setProp("lattice", value);
+        },
+        get derivedProperties() {
+            return this.prop("derivedProperties");
+        },
+        set derivedProperties(value) {
+            this.setProp("derivedProperties", value);
+        },
+        get external() {
+            return this.prop("external");
+        },
+        set external(value) {
+            this.setProp("external", value);
+        },
+        get src() {
+            return this.prop("src");
+        },
+        set src(value) {
+            this.setProp("src", value);
+        },
+        get scaledHash() {
+            return this.prop("scaledHash");
+        },
+        set scaledHash(value) {
+            this.setProp("scaledHash", value);
+        },
+        get icsdId() {
+            return this.prop("icsdId");
+        },
+        set icsdId(value) {
+            this.setProp("icsdId", value);
+        },
+        get isNonPeriodic() {
+            return this.prop("isNonPeriodic");
+        },
+        set isNonPeriodic(value) {
+            this.setProp("isNonPeriodic", value);
+        },
+        get consistencyChecks() {
+            return this.prop("consistencyChecks");
+        },
+        set consistencyChecks(value) {
+            this.setProp("consistencyChecks", value);
+        },
+    };
+    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}
+exports.materialSchemaMixin = materialSchemaMixin;

dist/js/lattice/lattice.d.ts

@@ -1,5 +1,5 @@
 import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import { LatticeSchema, LatticeTypeEnum, LatticeTypeExtendedEnum, LatticeVectorsSchema, Matrix3X3Schema } from "@mat3ra/esse/dist/js/types";
+import { BaseInMemoryEntitySchema, LatticeSchema, LatticeTypeEnum, LatticeTypeExtendedEnum, LatticeVectorsSchema, Matrix3X3Schema } from "@mat3ra/esse/dist/js/types";
 import { Cell } from "../cell/cell";
 import { UnitCell } from "./unit_cell";
 /**
@@ -10,7 +10,8 @@ export { defaultNonPeriodicMinimumLatticeSize, diatomicLatticePaddingFactor, mol
 export declare class LatticeVectors extends Cell implements LatticeVectorsSchema {
 }
 export type { LatticeVectorsSchema };
-export declare class Lattice extends InMemoryEntity implements LatticeSchema {
+type LatticeEntitySchema = LatticeSchema & BaseInMemoryEntitySchema;
+export declare class Lattice extends InMemoryEntity<LatticeEntitySchema> implements LatticeSchema {
     static defaultConfig: LatticeSchema;
     a: LatticeSchema["a"];
     b: LatticeSchema["b"];
@@ -63,5 +64,5 @@ export declare class Lattice extends InMemoryEntity implements LatticeSchema {
      * @example {a: true, b: false, c: false, alpha: true, beta: false, gamma: false}
      */
     get editables(): {};
-    toJSON(exclude?: string[]): LatticeSchema;
+    toJSON(exclude?: (keyof LatticeSchema)[]): LatticeSchema;
 }

dist/js/lattice/lattice.js

@@ -246,8 +246,7 @@ class Lattice extends entity_1.InMemoryEntity {
         }
         return object;
     }
-    // @ts-ignore
-    toJSON(exclude) {
+    toJSON(exclude = []) {
         return {
             ...super.toJSON(exclude),
             vectors: this.vectors.toJSON(),

dist/js/made.d.ts

@@ -33,7 +33,7 @@ export declare const Made: {
         cartesian: string;
     };
     Material: typeof Material;
-    defaultMaterialConfig: import("@mat3ra/esse/dist/js/types").MaterialSchema;
+    defaultMaterialConfig: import("./material").MaterialConfig;
     Lattice: typeof Lattice;
     Cell: typeof Cell;
     UnitCell: typeof UnitCell;

dist/js/material.d.ts

@@ -1,38 +1,28 @@
-import { type DefaultableInMemoryEntity, InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import { type HasConsistencyChecks } from "@mat3ra/code/dist/js/entity/mixins/HasConsistencyChecksMixin";
+import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
+import { type Defaultable } from "@mat3ra/code/dist/js/entity/mixins/DefaultableMixin";
+import { type HashedEntity } from "@mat3ra/code/dist/js/entity/mixins/HashedEntityMixin";
 import { type HasMetadata } from "@mat3ra/code/dist/js/entity/mixins/HasMetadataMixin";
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
-import type { AtomicConstraintsSchema, ConsistencyCheck, DerivedPropertiesSchema, FileSourceSchema, LatticeSchema, MaterialSchema } from "@mat3ra/esse/dist/js/types";
+import { type NamedEntity } from "@mat3ra/code/dist/js/entity/mixins/NamedEntityMixin";
+import type { AtomicConstraintsSchema, BasisSchema, ConsistencyCheck, DerivedPropertiesSchema, FileSourceSchema, LatticeSchema, MaterialSchema } from "@mat3ra/esse/dist/js/types";
 import type { BasisConfig } from "./basis/basis";
-import { type ConstrainedBasisConfig, ConstrainedBasis } from "./basis/constrained_basis";
-import { Constraint } from "./constraints/constraints";
+import { ConstrainedBasis } from "./basis/constrained_basis";
+import { type MaterialSchemaMixin } from "./generated/MaterialSchemaMixin";
 import { Lattice } from "./lattice/lattice";
-interface Material extends HasConsistencyChecks, DefaultableInMemoryEntity, Required<HasMetadata<MaterialSchema["metadata"]>> {
+export type PartialBy<T, K extends keyof T> = Omit<T, K> & Partial<Pick<T, K>>;
+export type MaterialConfig = PartialBy<MaterialSchema, "name" | "metadata" | "hash">;
+export declare const defaultMaterialConfig: MaterialConfig;
+interface BaseMaterial extends MaterialSchemaMixin, NamedEntity, Defaultable, HashedEntity, Required<HasMetadata<MaterialSchema["metadata"]>> {
 }
-type MaterialSchemaWithConsistencyChecksAsString = Omit<MaterialSchema, "consistencyChecks"> & {
-    consistencyChecks?: ConsistencyCheck[];
-};
-type OptionallyConstrainedBasisConfig = BasisConfig & Partial<Pick<ConstrainedBasisConfig, "constraints">>;
-type Schema = MaterialSchemaWithConsistencyChecksAsString;
-export declare const defaultMaterialConfig: MaterialSchema;
-declare class Material extends InMemoryEntity implements Schema {
+declare class BaseMaterial extends InMemoryEntity<MaterialSchema> {
+}
+declare class Material extends BaseMaterial implements MaterialSchema {
     static createDefault: () => Material;
-    static get defaultConfig(): MaterialSchema;
+    static get defaultConfig(): MaterialConfig;
     static constructMaterialFileSource(fileName: string, fileContent: string, fileExtension: string): FileSourceSchema;
-    get name(): string;
-    set name(name: string);
-    get src(): FileSourceSchema | undefined;
-    set src(src: FileSourceSchema | undefined);
+    private constraints;
+    constructor(config: MaterialConfig, constraints?: AtomicConstraintsSchema);
     updateFormula(): void;
-    /**
-     * Gets Bolean value for whether or not a material is non-periodic vs periodic.
-     * False = periodic, True = non-periodic
-     */
-    get isNonPeriodic(): boolean;
-    /**
-     * @summary Sets the value of isNonPeriodic based on Boolean value passed as an argument.
-     */
-    set isNonPeriodic(bool: boolean);
+    updateHash(): void;
     /**
      * @summary Returns the specific derived property (as specified by name) for a material.
      */
@@ -71,29 +61,16 @@ declare class Material extends InMemoryEntity implements Schema {
      * @summary Returns the derived properties array for a material.
      */
     getDerivedProperties(): DerivedPropertiesSchema;
-    /**
-     * Gets material's formula
-     */
-    get formula(): string;
-    get unitCellFormula(): string;
     unsetFileProps(): void;
-    /**
-     * @param textOrObject Basis text or JSON object.
-     * @param format Format (xyz, etc.)
-     * @param unitz crystal/cartesian
-     */
-    setBasis(textOrObject: string | BasisConfig, format?: string, unitz?: string): void;
-    setBasisConstraints(constraints: Constraint[]): void;
-    setBasisConstraintsFromArrayOfObjects(constraints: AtomicConstraintsSchema): void;
-    get basis(): OptionallyConstrainedBasisConfig;
-    get Basis(): ConstrainedBasis;
+    setBasis(basis: BasisConfig): void;
+    setBasis(basis: string, format: "xyz", unitz?: BasisSchema["units"]): void;
+    getBasis(constraints?: AtomicConstraintsSchema): ConstrainedBasis;
+    setLattice(lattice: LatticeSchema): void;
+    getLattice(): Lattice;
     /**
      * High-level access to unique elements from material instead of basis.
      */
     get uniqueElements(): ("H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "S" | "Cl" | "Ar" | "K" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og" | "X" | "Vac")[];
-    get lattice(): LatticeSchema;
-    set lattice(config: LatticeSchema);
-    get Lattice(): Lattice;
     /**
      * Returns the inchi string from the derivedProperties for a non-periodic material, or throws an error if the
      *  inchi cannot be found.
@@ -111,23 +88,15 @@ declare class Material extends InMemoryEntity implements Schema {
      * @param isScaled Whether to scale the lattice parameter 'a' to 1.
      */
     calculateHash(salt?: string, isScaled?: boolean, bypassNonPeriodicCheck?: boolean): string;
-    set hash(hash: string);
-    get hash(): string;
-    /**
-     * Calculates hash from basis and lattice as above + scales lattice properties to make lattice.a = 1
-     */
-    get scaledHash(): string;
-    get external(): MaterialSchema["external"];
-    set external(external: MaterialSchema["external"]);
     /**
      * Converts basis to crystal/fractional coordinates.
      */
-    toCrystal(): void;
+    toCrystal(constraints?: AtomicConstraintsSchema): void;
     /**
      * Converts current material's basis coordinates to cartesian.
      * No changes if coordinates already cartesian.
      */
-    toCartesian(): void;
+    toCartesian(constraints?: AtomicConstraintsSchema): void;
     /**
      * Returns material's basis in XYZ format.
      */
@@ -164,6 +133,6 @@ declare class Material extends InMemoryEntity implements Schema {
      * @returns Array of checks results
      */
     getBasisConsistencyChecks(): ConsistencyCheck[];
-    toJSON(): MaterialSchema & AnyObject;
+    toJSON(): MaterialSchema;
 }
 export { Material };