@mat3ra/esse 2025.11.19-0 → 2025.11.25-1

package/dist/js/esse/JSONSchemasInterface.d.ts

@@ -28,4 +28,17 @@ export default class JSONSchemasInterface {
      * })
      */
     static matchSchema(query: JSONSchemasInterfaceQuery): import("json-schema").JSONSchema7 | undefined;
+    /**
+     * Get a patched copy of a schema without modifying the cached version
+     * @param schemaId - The ID of the schema to patch
+     * @param propertyPatches - Object with property names as keys and patch objects as values
+     * @returns A new schema with patched properties
+     *
+     * @example
+     * JSONSchemasInterface.getPatchedSchema("boundary-conditions-provider", {
+     *   type: { default: "pbc" },
+     *   offset: { default: 0 }
+     * });
+     */
+    static getPatchedSchemaById(schemaId: string, patchConfig: Record<string, unknown>): JSONSchema | undefined;
 }

package/dist/js/esse/JSONSchemasInterface.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const utils_1 = require("./utils");
 class JSONSchemasInterface {
     static setSchemas(schema) {
         schema.forEach((schema) => this.addSchema(schema));
@@ -43,6 +44,27 @@ class JSONSchemasInterface {
             });
         });
     }
+    /**
+     * Get a patched copy of a schema without modifying the cached version
+     * @param schemaId - The ID of the schema to patch
+     * @param propertyPatches - Object with property names as keys and patch objects as values
+     * @returns A new schema with patched properties
+     *
+     * @example
+     * JSONSchemasInterface.getPatchedSchema("boundary-conditions-provider", {
+     *   type: { default: "pbc" },
+     *   offset: { default: 0 }
+     * });
+     */
+    static getPatchedSchemaById(schemaId, patchConfig) {
+        const baseSchema = this.getSchemaById(schemaId);
+        if (!baseSchema) {
+            return undefined;
+        }
+        const patchedSchema = JSON.parse(JSON.stringify(baseSchema));
+        (0, utils_1.applyPatchTree)(patchedSchema, patchConfig, []);
+        return patchedSchema;
+    }
 }
 exports.default = JSONSchemasInterface;
 JSONSchemasInterface.schemasCache = new Map();

package/dist/js/esse/utils.d.ts

@@ -12,3 +12,5 @@ export interface JSONSchemaWithPath {
 }
 export declare function parseIncludeReferenceStatementsByDir(dirPath: string, wrapInDataAndPath: true): JSONSchemaWithPath[];
 export declare function parseIncludeReferenceStatementsByDir(dirPath: string, wrapInDataAndPath?: false): JSONSchema[];
+export declare function applyPatchWithDotNotation(target: Record<string, unknown>, path: string, patchValue: unknown): void;
+export declare function applyPatchTree(schema: Record<string, unknown>, patchNode: Record<string, unknown>, pathPrefix: string[]): void;

package/dist/js/esse/utils.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseIncludeReferenceStatementsByDir = exports.parseIncludeReferenceStatements = void 0;
+exports.applyPatchTree = exports.applyPatchWithDotNotation = exports.parseIncludeReferenceStatementsByDir = exports.parseIncludeReferenceStatements = void 0;
 // @ts-ignore
 const json_schema_deref_sync_1 = __importDefault(require("json-schema-deref-sync"));
 const path_1 = __importDefault(require("path"));
@@ -59,3 +59,52 @@ function parseIncludeReferenceStatementsByDir(dirPath, wrapInDataAndPath = false
     return wrapInDataAndPath ? schemasWithPath : schemas;
 }
 exports.parseIncludeReferenceStatementsByDir = parseIncludeReferenceStatementsByDir;
+function isPlainObject(value) {
+    return value !== null && typeof value === "object" && !Array.isArray(value);
+}
+function applyPatchWithDotNotation(target, path, patchValue) {
+    const keys = path.split(".");
+    let current = target;
+    // Navigate to parent of final key
+    for (let index = 0; index < keys.length - 1; index += 1) {
+        const key = keys[index];
+        if (!isPlainObject(current[key])) {
+            // Path does not exist or is not an object → skip patch
+            return;
+        }
+        current = current[key];
+    }
+    const finalKey = keys[keys.length - 1];
+    const existingValue = current[finalKey];
+    if (isPlainObject(existingValue) && isPlainObject(patchValue)) {
+        // Merge object into existing object
+        Object.assign(existingValue, patchValue);
+    }
+    else if (existingValue !== undefined) {
+        // Overwrite leaf value
+        current[finalKey] = patchValue;
+    }
+    // If existingValue is undefined, we skip;
+}
+exports.applyPatchWithDotNotation = applyPatchWithDotNotation;
+function applyPatchTree(schema, patchNode, pathPrefix) {
+    Object.entries(patchNode).forEach(([key, value]) => {
+        if (key.includes(".")) {
+            // Dot notation relative to current prefix
+            const fullPathSegments = [...pathPrefix, ...key.split(".")];
+            const fullPath = fullPathSegments.join(".");
+            applyPatchWithDotNotation(schema, fullPath, value);
+        }
+        else if (isPlainObject(value)) {
+            // Nested subtree → recurse with extended prefix
+            applyPatchTree(schema, value, [...pathPrefix, key]);
+        }
+        else {
+            // Leaf patch (primitive / array) → treat as direct field patch
+            const fullPathSegments = [...pathPrefix, key];
+            const fullPath = fullPathSegments.join(".");
+            applyPatchWithDotNotation(schema, fullPath, value);
+        }
+    });
+}
+exports.applyPatchTree = applyPatchTree;

package/dist/js/schema/context_provider.json

@@ -0,0 +1,93 @@
+{
+    "$id": "context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "context provider schema",
+    "type": "object",
+    "required": [
+        "name"
+    ],
+    "additionalProperties": true,
+    "properties": {
+        "name": {
+            "type": "string",
+            "enum": [
+                "PlanewaveCutoffDataManager",
+                "KGridFormDataManager",
+                "QGridFormDataManager",
+                "IGridFormDataManager",
+                "QPathFormDataManager",
+                "IPathFormDataManager",
+                "KPathFormDataManager",
+                "ExplicitKPathFormDataManager",
+                "ExplicitKPath2PIBAFormDataManager",
+                "HubbardJContextManager",
+                "HubbardUContextManager",
+                "HubbardVContextManager",
+                "HubbardContextManagerLegacy",
+                "NEBFormDataManager",
+                "BoundaryConditionsFormDataManager",
+                "MLSettingsDataManager",
+                "MLTrainTestSplitDataManager",
+                "IonDynamicsContextProvider",
+                "CollinearMagnetizationDataManager",
+                "NonCollinearMagnetizationDataManager",
+                "QEPWXInputDataManager",
+                "QENEBInputDataManager",
+                "VASPInputDataManager",
+                "VASPNEBInputDataManager",
+                "NWChemInputDataManager"
+            ],
+            "tsEnumNames": [
+                "PlanewaveCutoffDataManager",
+                "KGridFormDataManager",
+                "QGridFormDataManager",
+                "IGridFormDataManager",
+                "QPathFormDataManager",
+                "IPathFormDataManager",
+                "KPathFormDataManager",
+                "ExplicitKPathFormDataManager",
+                "ExplicitKPath2PIBAFormDataManager",
+                "HubbardJContextManager",
+                "HubbardUContextManager",
+                "HubbardVContextManager",
+                "HubbardContextManagerLegacy",
+                "NEBFormDataManager",
+                "BoundaryConditionsFormDataManager",
+                "MLSettingsDataManager",
+                "MLTrainTestSplitDataManager",
+                "IonDynamicsContextProvider",
+                "CollinearMagnetizationDataManager",
+                "NonCollinearMagnetizationDataManager",
+                "QEPWXInputDataManager",
+                "QENEBInputDataManager",
+                "VASPInputDataManager",
+                "VASPNEBInputDataManager",
+                "NWChemInputDataManager"
+            ]
+        },
+        "domain": {
+            "description": "domain of the context provider",
+            "type": "string"
+        },
+        "entityName": {
+            "description": "entity name associated with the context provider",
+            "type": "string"
+        },
+        "data": {
+            "description": "data object for the context provider",
+            "type": "object"
+        },
+        "extraData": {
+            "description": "additional data object for the context provider",
+            "type": "object"
+        },
+        "isEdited": {
+            "description": "flag indicating if the context provider has been edited",
+            "type": "boolean"
+        },
+        "context": {
+            "description": "context object for the context provider",
+            "type": "object"
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/boundary_conditions_data_provider.json

@@ -0,0 +1,30 @@
+{
+    "$id": "context-providers-directory/boundary-conditions-data-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Boundary Conditions Provider Schema",
+    "type": "object",
+    "properties": {
+        "type": {
+            "type": "string",
+            "enum": [
+                "pbc",
+                "bc1",
+                "bc2",
+                "bc3"
+            ],
+            "default": "pbc",
+            "description": "If assume_isolated = 'esm', determines the boundary conditions used for either side of the slab."
+        },
+        "offset": {
+            "type": "number"
+        },
+        "electricField": {
+            "type": "number",
+            "title": "Electric Field (eV/A)"
+        },
+        "targetFermiEnergy": {
+            "type": "number",
+            "title": "Target Fermi Energy (eV)"
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/collinear_magnetization_context_provider.json

@@ -0,0 +1,35 @@
+{
+    "$id": "context-providers-directory/collinear-magnetization-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Collinear Magnetization Provider Schema",
+    "description": "Set starting magnetization, can have values in the range [-1, +1].",
+    "type": "object",
+    "properties": {
+        "startingMagnetization": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "atomicSpecies": {
+                        "type": "string",
+                        "title": "Atomic species"
+                    },
+                    "value": {
+                        "type": "number",
+                        "title": "Starting magnetization",
+                        "minimum": -1,
+                        "maximum": 1
+                    }
+                }
+            }
+        },
+        "isTotalMagnetization": {
+            "type": "boolean",
+            "title": "Set total magnetization instead"
+        },
+        "totalMagnetization": {
+            "type": "number",
+            "title": "Total magnetization"
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/enum.json

@@ -0,0 +1,62 @@
+{
+    "$id": "context-providers-directory/enum",
+    "definitions": {
+        "ContextProviderNameEnum": {
+            "type": "string",
+            "enum": [
+                "PlanewaveCutoffDataManager",
+                "KGridFormDataManager",
+                "QGridFormDataManager",
+                "IGridFormDataManager",
+                "QPathFormDataManager",
+                "IPathFormDataManager",
+                "KPathFormDataManager",
+                "ExplicitKPathFormDataManager",
+                "ExplicitKPath2PIBAFormDataManager",
+                "HubbardJContextManager",
+                "HubbardUContextManager",
+                "HubbardVContextManager",
+                "HubbardContextManagerLegacy",
+                "NEBFormDataManager",
+                "BoundaryConditionsFormDataManager",
+                "MLSettingsDataManager",
+                "MLTrainTestSplitDataManager",
+                "IonDynamicsContextProvider",
+                "CollinearMagnetizationDataManager",
+                "NonCollinearMagnetizationDataManager",
+                "QEPWXInputDataManager",
+                "QENEBInputDataManager",
+                "VASPInputDataManager",
+                "VASPNEBInputDataManager",
+                "NWChemInputDataManager"
+            ],
+            "tsEnumNames": [
+                "PlanewaveCutoffDataManager",
+                "KGridFormDataManager",
+                "QGridFormDataManager",
+                "IGridFormDataManager",
+                "QPathFormDataManager",
+                "IPathFormDataManager",
+                "KPathFormDataManager",
+                "ExplicitKPathFormDataManager",
+                "ExplicitKPath2PIBAFormDataManager",
+                "HubbardJContextManager",
+                "HubbardUContextManager",
+                "HubbardVContextManager",
+                "HubbardContextManagerLegacy",
+                "NEBFormDataManager",
+                "BoundaryConditionsFormDataManager",
+                "MLSettingsDataManager",
+                "MLTrainTestSplitDataManager",
+                "IonDynamicsContextProvider",
+                "CollinearMagnetizationDataManager",
+                "NonCollinearMagnetizationDataManager",
+                "QEPWXInputDataManager",
+                "QENEBInputDataManager",
+                "VASPInputDataManager",
+                "VASPNEBInputDataManager",
+                "NWChemInputDataManager"
+            ]
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/hubbard_j_context_provider.json

@@ -0,0 +1,36 @@
+{
+    "$id": "context-providers-directory/hubbard-j-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Hubbard J Provider Schema",
+    "description": "Hubbard parameters for DFT+U+J calculation.",
+    "type": "array",
+    "minItems": 1,
+    "items": {
+        "type": "object",
+        "properties": {
+            "paramType": {
+                "type": "string",
+                "title": "Species",
+                "enum": [
+                    "U",
+                    "J",
+                    "B",
+                    "E2",
+                    "E3"
+                ]
+            },
+            "atomicSpecies": {
+                "type": "string",
+                "title": "Species"
+            },
+            "atomicOrbital": {
+                "type": "string",
+                "title": "Orbital"
+            },
+            "value": {
+                "type": "number",
+                "title": "Value (eV)"
+            }
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/hubbard_legacy_context_provider.json

@@ -0,0 +1,26 @@
+{
+    "$id": "context-providers-directory/hubbard-legacy-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Hubbard Legacy Provider Schema",
+    "description": "Hubbard parameters for DFT+U calculation.",
+    "type": "array",
+    "uniqueItems": true,
+    "minItems": 1,
+    "items": {
+        "type": "object",
+        "properties": {
+            "atomicSpecies": {
+                "type": "string",
+                "title": "Atomic species"
+            },
+            "atomicSpeciesIndex": {
+                "type": "integer",
+                "title": "Species index"
+            },
+            "hubbardUValue": {
+                "type": "number",
+                "title": "Hubbard U (eV)"
+            }
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/hubbard_u_context_provider.json

@@ -0,0 +1,24 @@
+{
+    "$id": "context-providers-directory/hubbard-u-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Hubbard U Provider Schema",
+    "description": "Hubbard U parameters for DFT+U or DFT+U+V calculation.",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "atomicSpecies": {
+                "type": "string",
+                "title": "Atomic species"
+            },
+            "atomicOrbital": {
+                "type": "string",
+                "title": "Atomic orbital"
+            },
+            "hubbardUValue": {
+                "type": "number",
+                "title": "Hubbard U (eV)"
+            }
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/hubbard_v_context_provider.json

@@ -0,0 +1,41 @@
+{
+    "$id": "context-providers-directory/hubbard-v-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Hubbard V Provider Schema",
+    "description": "Hubbard V parameters for DFT+U+V calculation.",
+    "type": "array",
+    "minItems": 1,
+    "items": {
+        "type": "object",
+        "properties": {
+            "atomicSpecies": {
+                "type": "string",
+                "title": "Species 1"
+            },
+            "siteIndex": {
+                "type": "integer",
+                "title": "Site no 1"
+            },
+            "atomicOrbital": {
+                "type": "string",
+                "title": "Orbital 1"
+            },
+            "atomicSpecies2": {
+                "type": "string",
+                "title": "Species 2"
+            },
+            "siteIndex2": {
+                "type": "integer",
+                "title": "Site no 2"
+            },
+            "atomicOrbital2": {
+                "type": "string",
+                "title": "Orbital 2"
+            },
+            "hubbardVValue": {
+                "type": "number",
+                "title": "V (eV)"
+            }
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/ion_dynamics_context_provider.json

@@ -0,0 +1,25 @@
+{
+    "$id": "context-providers-directory/ion-dynamics-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Ion Dynamics Provider Schema",
+    "description": "Important parameters for molecular dynamics calculation",
+    "type": "object",
+    "properties": {
+        "numberOfSteps": {
+            "type": "integer",
+            "title": "numberOfSteps"
+        },
+        "timeStep": {
+            "type": "number",
+            "title": "timeStep (Hartree a.u.)"
+        },
+        "electronMass": {
+            "type": "number",
+            "title": "Effective electron mass"
+        },
+        "temperature": {
+            "type": "number",
+            "title": "Ionic temperature (K)"
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/ml_settings_context_provider.json

@@ -0,0 +1,20 @@
+{
+    "$id": "context-providers-directory/ml-settings-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "ML Settings Provider Schema",
+    "description": "Settings important to machine learning runs.",
+    "type": "object",
+    "properties": {
+        "target_column_name": {
+            "type": "string"
+        },
+        "problem_category": {
+            "type": "string",
+            "enum": [
+                "regression",
+                "classification",
+                "clustering"
+            ]
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/ml_train_test_split_context_provider.json

@@ -0,0 +1,14 @@
+{
+    "$id": "context-providers-directory/ml-train-test-split-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "ML Train Test Split Provider Schema",
+    "description": "Fraction held as the test set. For example, a value of 0.2 corresponds to an 80/20 train/test split.",
+    "type": "object",
+    "properties": {
+        "fraction_held_as_test_set": {
+            "type": "number",
+            "minimum": 0,
+            "maximum": 1
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/neb_data_provider.json

@@ -0,0 +1,12 @@
+{
+    "$id": "context-providers-directory/neb-data-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "NEB Provider Schema",
+    "description": "Number of intermediate NEB images.",
+    "type": "object",
+    "properties": {
+        "nImages": {
+            "type": "number"
+        }
+    }
+}

package/dist/js/schema/context_providers_directory/non_collinear_magnetization_context_provider.json

@@ -0,0 +1,110 @@
+{
+    "$id": "context-providers-directory/non-collinear-magnetization-context-provider",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Non Collinear Magnetization Provider Schema",
+    "description": "Non-collinear magnetization parameters including starting magnetization, spin angles, and constraints.",
+    "type": "object",
+    "properties": {
+        "isExistingChargeDensity": {
+            "type": "boolean",
+            "title": "Use existing charge density"
+        },
+        "isStartingMagnetization": {
+            "type": "boolean",
+            "title": "Set starting magnetization"
+        },
+        "startingMagnetization": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "index": {
+                        "type": "integer",
+                        "title": "Index"
+                    },
+                    "atomicSpecies": {
+                        "type": "string",
+                        "title": "Atomic species"
+                    },
+                    "value": {
+                        "type": "number",
+                        "title": "Starting magnetization"
+                    }
+                }
+            }
+        },
+        "isArbitrarySpinAngle": {
+            "type": "boolean",
+            "title": "Set arbitrary spin angle"
+        },
+        "spinAngles": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "index": {
+                        "type": "integer",
+                        "title": "Index"
+                    },
+                    "atomicSpecies": {
+                        "type": "string",
+                        "title": "Atomic species"
+                    },
+                    "angle1": {
+                        "type": "number",
+                        "title": "Angle1 (deg)"
+                    },
+                    "angle2": {
+                        "type": "number",
+                        "title": "Angle2 (deg)"
+                    }
+                }
+            }
+        },
+        "isConstrainedMagnetization": {
+            "type": "boolean",
+            "title": "Set constrained magnetization"
+        },
+        "constrainedMagnetization": {
+            "type": "object",
+            "properties": {
+                "constrainType": {
+                    "type": "string",
+                    "title": "Constrain type",
+                    "enum": [
+                        "none",
+                        "total",
+                        "atomic",
+                        "total direction",
+                        "atomic direction"
+                    ]
+                },
+                "lambda": {
+                    "type": "number",
+                    "title": "lambda"
+                }
+            }
+        },
+        "isFixedMagnetization": {
+            "type": "boolean",
+            "title": "Set Fixed magnetization (only applicable to constrained magnetization of 'total' type)"
+        },
+        "fixedMagnetization": {
+            "type": "object",
+            "properties": {
+                "x": {
+                    "type": "number",
+                    "title": "X-component"
+                },
+                "y": {
+                    "type": "number",
+                    "title": "Y-component"
+                },
+                "z": {
+                    "type": "number",
+                    "title": "Z-component"
+                }
+            }
+        }
+    }
+}