@mat3ra/esse 2025.4.26-0 → 2025.5.16-0

package/.eslintrc.json

@@ -1,11 +1,5 @@
 {
-    "extends": ["@exabyte-io/eslint-config"],
-    "ignorePatterns": ["dist/js/**/*.js", "dist/js/**/*.ts", "src/js/types.ts"],
-    "settings": {
-        "import/resolver": {
-          "node": {
-            "extensions": [".js", ".jsx", ".ts", ".tsx"]
-          }
-        }
-    }
+    "extends": [
+        "@exabyte-io/eslint-config/json"
+    ]
 }

package/.prettierrc

@@ -2,5 +2,6 @@
     "singleQuote": false,
     "printWidth": 100,
     "trailingComma": "all",
-    "tabWidth": 4
+    "tabWidth": 4,
+    "bracketSpacing": true
 }

package/dist/js/esse/JSONSchemasGenerator.js

@@ -39,10 +39,18 @@ class JSONSchemasGenerator {
             resolvers: { defaultResolver: json_schema_merge_allof_1.default.options.resolvers.title },
         };
         const schemas = this.schemas.map((schema) => {
-            var _a;
             console.log(`Resolving schema: ${schema.$id}`);
             const mergedSchema = skipMergeAllOff ? schema : (0, json_schema_merge_allof_1.default)(schema, mergeAllOfConfig);
-            const idAsPath = (_a = mergedSchema.$id) === null || _a === void 0 ? void 0 : _a.replace(/-/g, "_");
+            let idAsPath = mergedSchema.$id;
+            if (!idAsPath) {
+                throw new Error(`Schema ID is missing:
+                ${JSON.stringify(mergedSchema)}`);
+            }
+            const schemaHasDash = idAsPath.includes("-");
+            if (schemaHasDash) {
+                // replace dashes with underscores
+                idAsPath = idAsPath.replace(/-/g, "_");
+            }
             const fullPath = `${schemasFolder}/${idAsPath}.json`;
             fs_1.default.mkdirSync(path_1.default.dirname(fullPath), { recursive: true });
             fs_1.default.writeFileSync(fullPath, JSON.stringify(mergedSchema, null, 4), "utf8");

package/dist/js/esse/utils.js

@@ -17,11 +17,17 @@ function parseIncludeReferenceStatements(filePath) {
     const jsonResolver = new json_include_1.JSONInclude();
     const parsed = jsonResolver.parseIncludeStatements(filePath);
     const dirPath = path_1.default.dirname(filePath);
+    // Store the original $id before dereferencing
+    const originalId = parsed.$id;
     let dereferenced = (0, json_schema_deref_sync_1.default)(parsed, { baseFolder: dirPath, removeIds: true });
     // handle circular references and use non-dereferenced source
     if (dereferenced instanceof Error && dereferenced.message === "Circular self reference") {
         dereferenced = parsed;
     }
+    // Restore the original $id after dereferencing
+    if (originalId) {
+        dereferenced.$id = originalId;
+    }
     return dereferenced;
 }
 exports.parseIncludeReferenceStatements = parseIncludeReferenceStatements;

package/dist/js/example/apse/materials/builders/slab/pymatgen/parameters.json

@@ -0,0 +1,6 @@
+{
+    "min_vacuum_size": 1,
+    "in_unit_planes": true,
+    "reorient_lattice": true,
+    "symmetrize": false
+}

package/dist/js/example/material/builders/base/selector_parameters.json

@@ -0,0 +1,3 @@
+{
+    "default_index": 0
+}

package/dist/js/example/material/builders/single_material/two_dimensional/slab/selector_parameters.json

@@ -0,0 +1,6 @@
+{
+    "termination": {
+        "chemical_elements": "C",
+        "space_group_symmetry_label": "P6/mmm"
+    }
+}

package/dist/js/example/material/reusable/repetitions.json

@@ -0,0 +1,5 @@
+[
+    1,
+    2,
+    3
+]

package/dist/js/example/material/reusable/slab/miller_indices.json

@@ -0,0 +1,5 @@
+[
+    0,
+    0,
+    1
+]

package/dist/js/example/material/reusable/slab/number_of_layers.json

@@ -0,0 +1 @@
+3

package/dist/js/example/material/reusable/slab/termination.json

@@ -0,0 +1,4 @@
+{
+    "chemical_elements": "Si",
+    "space_group_symmetry_label": "P4/mmm_2"
+}

package/dist/js/example/material/reusable/slab/vacuum.json

@@ -0,0 +1 @@
+15

package/dist/js/example/material/reusable/supercell_matrix_2d.json

@@ -0,0 +1,10 @@
+[
+    [
+        2,
+        0
+    ],
+    [
+        0,
+        2
+    ]
+]

package/dist/js/example/material/reusable/supercell_matrix_3d.json

@@ -0,0 +1,17 @@
+[
+    [
+        1,
+        0,
+        0
+    ],
+    [
+        0,
+        2,
+        0
+    ],
+    [
+        0,
+        0,
+        3
+    ]
+]

package/dist/js/example/materials_category/single_material/two_dimensional/slab/configuration.json

@@ -0,0 +1,150 @@
+{
+    "bulk": {
+        "_id": "LCthJ6E2QabYCZqf3",
+        "basis": {
+            "coordinates": [
+                {
+                    "id": 1,
+                    "value": [
+                        0,
+                        0,
+                        0
+                    ]
+                },
+                {
+                    "id": 2,
+                    "value": [
+                        0.25,
+                        0.25,
+                        0.25
+                    ]
+                }
+            ],
+            "elements": [
+                {
+                    "id": 1,
+                    "value": "Si"
+                },
+                {
+                    "id": 2,
+                    "value": "Si"
+                }
+            ],
+            "name": "basis",
+            "units": "crystal"
+        },
+        "createdAt": "2016-04-03T05:25:37.430Z",
+        "creator": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "User",
+            "slug": "exadmin"
+        },
+        "derivedProperties": [
+            {
+                "name": "volume",
+                "units": "angstrom^3",
+                "value": 131.1
+            },
+            {
+                "name": "density",
+                "units": "g/cm^3",
+                "value": 2.33
+            },
+            {
+                "name": "symmetry",
+                "spaceGroupSymbol": "Fd-3m",
+                "tolerance": {
+                    "units": "angstrom",
+                    "value": 0.3
+                }
+            },
+            {
+                "degree": 10,
+                "name": "p-norm",
+                "value": 0.71
+            },
+            {
+                "element": "Si",
+                "name": "elemental_ratio",
+                "value": 0.71
+            },
+            {
+                "name": "inchi",
+                "value": ""
+            },
+            {
+                "name": "inchi_key",
+                "value": ""
+            }
+        ],
+        "exabyteId": "RKiswuxHKkF3uvLyA",
+        "formula": "Si",
+        "hash": "4ac3fa057e3530628eb1295c77110eaa",
+        "isDefault": false,
+        "isNonPeriodic": false,
+        "lattice": {
+            "name": "lattice",
+            "a": 5.14,
+            "alpha": 90,
+            "b": 5.14,
+            "beta": 90,
+            "c": 5.14,
+            "gamma": 90,
+            "type": "CUB",
+            "units": {
+                "angle": "degree",
+                "length": "angstrom"
+            },
+            "vectors": {
+                "a": [
+                    5,
+                    0.000121312,
+                    0.000131415
+                ],
+                "alat": 1,
+                "b": [
+                    0.000121312,
+                    5,
+                    0.000121314
+                ],
+                "c": [
+                    0.000121313,
+                    0.000121312,
+                    5
+                ],
+                "units": "angstrom"
+            }
+        },
+        "name": "Silicon FCC",
+        "owner": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "Account",
+            "slug": "exabyte"
+        },
+        "scaledHash": "5bd4eb168e3530628eb1295d88221cbb",
+        "schemaVersion": "0.2.0",
+        "slug": "silicon-fcc",
+        "unitCellFormula": "Si2",
+        "updatedAt": "2016-04-04T17:58:42.867Z"
+    },
+    "miller_indices": [
+        0,
+        0,
+        1
+    ],
+    "number_of_layers": 3,
+    "vacuum": 15,
+    "xy_supercell_matrix": [
+        [
+            1,
+            0
+        ],
+        [
+            0,
+            1
+        ]
+    ],
+    "use_conventional_cell": true,
+    "use_orthogonal_z": true,
+    "make_primitive": true
+}

package/dist/js/schema/apse/materials/builders/slab/pymatgen/parameters.json

@@ -0,0 +1,33 @@
+{
+    "$id": "apse/materials/builders/slab/pymatgen/parameters",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Pymatgen Slab Generator Parameters Schema",
+    "description": "Parameters for the Pymatgen slab generator. https://github.com/materialsproject/pymatgen/blob/585bb673c4aa222669c4b0d72ffeec3dbf092630/pymatgen/core/surface.py#L1187",
+    "type": "object",
+    "properties": {
+        "min_vacuum_size": {
+            "description": "Minimum size of the vacuum in layers or angstroms",
+            "type": [
+                "integer",
+                "number"
+            ],
+            "minimum": 0,
+            "default": 1
+        },
+        "in_unit_planes": {
+            "description": "Whether to cleave in unit planes",
+            "type": "boolean",
+            "default": true
+        },
+        "reorient_lattice": {
+            "description": "Whether to reorient the lattice",
+            "type": "boolean",
+            "default": true
+        },
+        "symmetrize": {
+            "description": "Whether to symmetrize the slab",
+            "type": "boolean",
+            "default": true
+        }
+    }
+}

package/dist/js/schema/core/abstract/coordinate_2d.json

@@ -0,0 +1,11 @@
+{
+    "$id": "core/abstract/coordinate-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "coordinate 2d schema",
+    "type": "array",
+    "minItems": 2,
+    "maxItems": 2,
+    "items": {
+        "type": "number"
+    }
+}

package/dist/js/schema/material/builders/base/selector_parameters.json

@@ -0,0 +1,15 @@
+{
+    "$id": "material/builders/base/selector-parameters",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Base Selector Parameters Schema",
+    "description": "Base parameters for all builder selectors",
+    "type": "object",
+    "properties": {
+        "default_index": {
+            "description": "Default index for the selector",
+            "type": "integer",
+            "minimum": 0,
+            "default": 0
+        }
+    }
+}

package/dist/js/schema/material/builders/single_material/two_dimensional/slab/builder_parameters.json

@@ -0,0 +1,33 @@
+{
+    "$id": "material/builders/single-material/two-dimensional/slab/builder-parameters",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Builder Parameters Schema",
+    "description": "Parameters for the slab builder",
+    "type": "object",
+    "properties": {
+        "min_vacuum_size": {
+            "description": "Minimum size of the vacuum in layers or angstroms",
+            "type": [
+                "integer",
+                "number"
+            ],
+            "minimum": 0,
+            "default": 1
+        },
+        "in_unit_planes": {
+            "description": "Whether to cleave in unit planes",
+            "type": "boolean",
+            "default": true
+        },
+        "reorient_lattice": {
+            "description": "Whether to reorient the lattice",
+            "type": "boolean",
+            "default": true
+        },
+        "symmetrize": {
+            "description": "Whether to symmetrize the slab",
+            "type": "boolean",
+            "default": true
+        }
+    }
+}

package/dist/js/schema/material/builders/single_material/two_dimensional/slab/selector_parameters.json

@@ -0,0 +1,31 @@
+{
+    "$id": "material/builders/single-material/two-dimensional/slab/selector-parameters",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Selector Parameters Schema",
+    "description": "Parameters for slab selection",
+    "type": "object",
+    "properties": {
+        "termination": {
+            "$schema": "http://json-schema.org/draft-07/schema#",
+            "title": "Termination Schema",
+            "description": "Defines a specific termination of a slab",
+            "type": "object",
+            "required": [
+                "chemical_elements",
+                "space_group_symmetry_label"
+            ],
+            "properties": {
+                "chemical_elements": {
+                    "title": "Chemical Elements",
+                    "description": "Chemical elements at the termination",
+                    "type": "string"
+                },
+                "space_group_symmetry_label": {
+                    "title": "Space Group Symmetry Label",
+                    "description": "Space group symmetry designation for the termination",
+                    "type": "string"
+                }
+            }
+        }
+    }
+}

package/dist/js/schema/material/reusable/repetitions.json

@@ -0,0 +1,18 @@
+{
+    "$id": "material/reusable/repetitions",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Repetitions Schema",
+    "description": "Number of unit cells to repeat in each direction for a crystal structure.",
+    "type": "array",
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        1,
+        1,
+        1
+    ],
+    "items": {
+        "type": "integer",
+        "minimum": 1
+    }
+}

package/dist/js/schema/material/reusable/slab/enums.json

@@ -0,0 +1,11 @@
+{
+    "$id": "material/reusable/slab/enums",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Surface Types Enum",
+    "$comment": "The surface types used by passivation and surface analysis",
+    "enum": [
+        "top",
+        "bottom",
+        "both"
+    ]
+}

package/dist/js/schema/material/reusable/slab/miller_indices.json

@@ -0,0 +1,17 @@
+{
+    "$id": "material/reusable/slab/miller-indices",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Miller Indices Schema",
+    "description": "Miller indices for crystallographic plane designation",
+    "type": "array",
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        0,
+        0,
+        1
+    ],
+    "items": {
+        "type": "integer"
+    }
+}

package/dist/js/schema/material/reusable/slab/number_of_layers.json

@@ -0,0 +1,9 @@
+{
+    "$id": "material/reusable/slab/number-of-layers",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "number_of_layers Schema",
+    "description": "Number of atomic layers in a structural component",
+    "type": "integer",
+    "minimum": 1,
+    "default": 1
+}

package/dist/js/schema/material/reusable/slab/termination.json

@@ -0,0 +1,23 @@
+{
+    "$id": "material/reusable/slab/termination",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Termination Schema",
+    "description": "Defines a specific termination of a slab",
+    "type": "object",
+    "required": [
+        "chemical_elements",
+        "space_group_symmetry_label"
+    ],
+    "properties": {
+        "chemical_elements": {
+            "title": "Chemical Elements",
+            "description": "Chemical elements at the termination",
+            "type": "string"
+        },
+        "space_group_symmetry_label": {
+            "title": "Space Group Symmetry Label",
+            "description": "Space group symmetry designation for the termination",
+            "type": "string"
+        }
+    }
+}

package/dist/js/schema/material/reusable/slab/vacuum.json

@@ -0,0 +1,9 @@
+{
+    "$id": "material/reusable/slab/vacuum",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Vacuum Schema",
+    "description": "Vacuum thickness in Angstroms",
+    "type": "number",
+    "minimum": 0,
+    "default": 5
+}

package/dist/js/schema/material/reusable/supercell_matrix_2d.json

@@ -0,0 +1,27 @@
+{
+    "$id": "material/reusable/supercell-matrix-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Supercell Matrix 2D Schema",
+    "description": "Supercell matrix for xy plane transformations",
+    "type": "array",
+    "minItems": 2,
+    "maxItems": 2,
+    "default": [
+        [
+            1,
+            0
+        ],
+        [
+            0,
+            1
+        ]
+    ],
+    "items": {
+        "type": "array",
+        "minItems": 2,
+        "maxItems": 2,
+        "items": {
+            "type": "integer"
+        }
+    }
+}

package/dist/js/schema/material/reusable/supercell_matrix_3d.json

@@ -0,0 +1,34 @@
+{
+    "$id": "material/reusable/supercell-matrix-3d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Supercell Matrix 3D Schema",
+    "description": "3x3 matrix of integers for transforming a unit cell into a supercell",
+    "type": "array",
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        [
+            1,
+            0,
+            0
+        ],
+        [
+            0,
+            1,
+            0
+        ],
+        [
+            0,
+            0,
+            1
+        ]
+    ],
+    "items": {
+        "type": "array",
+        "minItems": 3,
+        "maxItems": 3,
+        "items": {
+            "type": "integer"
+        }
+    }
+}