@mat3ra/esse 2026.5.18-2 → 2026.5.27-0

package/dist/js/types.js

@@ -29,7 +29,7 @@ var Name;
     Name["VASPInputDataManager"] = "VASPInputDataManager";
     Name["VASPNEBInputDataManager"] = "VASPNEBInputDataManager";
     Name["NWChemInputDataManager"] = "NWChemInputDataManager";
-})(Name || (exports.Name = Name = {}));
+})(Name = exports.Name || (exports.Name = {}));
 /**
  * This interface was referenced by `ContextProvidersDirectoryEnum`'s JSON-Schema
  * via the `definition` "ContextProviderNameEnum".
@@ -61,7 +61,7 @@ var ContextProviderNameEnum;
     ContextProviderNameEnum["VASPInputDataManager"] = "VASPInputDataManager";
     ContextProviderNameEnum["VASPNEBInputDataManager"] = "VASPNEBInputDataManager";
     ContextProviderNameEnum["NWChemInputDataManager"] = "NWChemInputDataManager";
-})(ContextProviderNameEnum || (exports.ContextProviderNameEnum = ContextProviderNameEnum = {}));
+})(ContextProviderNameEnum = exports.ContextProviderNameEnum || (exports.ContextProviderNameEnum = {}));
 /**
  * The type of the message to distinguish the direction of the message.
  */
@@ -69,7 +69,7 @@ var Type;
 (function (Type) {
     Type["fromIframeToHost"] = "from-iframe-to-host";
     Type["fromHostToIframe"] = "from-host-to-iframe";
-})(Type || (exports.Type = Type = {}));
+})(Type = exports.Type || (exports.Type = {}));
 /**
  * The action to be performed upon receiving the message.
  */
@@ -78,7 +78,7 @@ var Action;
     Action["setData"] = "set-data";
     Action["getData"] = "get-data";
     Action["info"] = "info";
-})(Action || (exports.Action = Action = {}));
+})(Action = exports.Action || (exports.Action = {}));
 /**
  * This interface was referenced by `WorkflowSubworkflowConvergenceEnumOptions`'s JSON-Schema
  * via the `definition` "ConvergenceParameterNameEnum".
@@ -88,4 +88,4 @@ var ConvergenceParameterNameEnum;
     ConvergenceParameterNameEnum["N_k"] = "N_k";
     ConvergenceParameterNameEnum["N_k_nonuniform"] = "N_k_nonuniform";
     ConvergenceParameterNameEnum["N_k_nonuniform_2D"] = "N_k_nonuniform_2D";
-})(ConvergenceParameterNameEnum || (exports.ConvergenceParameterNameEnum = ConvergenceParameterNameEnum = {}));
+})(ConvergenceParameterNameEnum = exports.ConvergenceParameterNameEnum || (exports.ConvergenceParameterNameEnum = {}));

package/dist/js/utils/ajv.js

@@ -3,9 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getValidator = getValidator;
-exports.validate = validate;
-exports.validateAndClean = validateAndClean;
+exports.validateAndClean = exports.validate = exports.getValidator = void 0;
 const ajv_1 = __importDefault(require("ajv"));
 const ajv_formats_1 = __importDefault(require("ajv-formats"));
 const schemaUtils_1 = require("../esse/schemaUtils");
@@ -25,7 +23,7 @@ function addAdditionalPropertiesToSchema(schema, additionalProperties = false) {
     });
 }
 const ajvConfig = {
-    strict: false, // TODO: adjust schemas and enable strict mode
+    strict: false,
     useDefaults: true,
     /**
      * discriminator fixes default values in oneOf
@@ -82,6 +80,7 @@ function getValidator(jsonSchema, { clean, coerceTypes, useDefaults = true, }) {
     }
     return validate;
 }
+exports.getValidator = getValidator;
 /**
  * Validates a given example against the schema.
  * @param example example to validate.
@@ -96,6 +95,7 @@ function validate(data, jsonSchema) {
         errors: validator.errors,
     };
 }
+exports.validate = validate;
 /**
  * Validates and clean a given example against the schema
  * @param example example to validate.
@@ -110,3 +110,4 @@ function validateAndClean(data, jsonSchema, { coerceTypes = false, useDefaults =
         errors: validator.errors,
     };
 }
+exports.validateAndClean = validateAndClean;

package/dist/js/utils/common.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isInstanceOf = isInstanceOf;
-exports.safeParseJSON = safeParseJSON;
+exports.safeParseJSON = exports.isInstanceOf = void 0;
 function isInstanceOf(object, type) {
     return Object.prototype.toString.call(object).slice(8, -1) === type;
 }
+exports.isInstanceOf = isInstanceOf;
 /**
  * Makes sure that text representing arrays is parsed into Arrays.
  */
@@ -12,3 +12,4 @@ function safeParseJSON(string) {
     const obj = JSON.parse(string);
     return string[0] === "[" ? Object.keys(obj).map((key) => obj[key]) : obj;
 }
+exports.safeParseJSON = safeParseJSON;

package/dist/js/utils/filesystem.js

@@ -3,8 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.walkDir = walkDir;
-exports.walkDirSync = walkDirSync;
+exports.walkDirSync = exports.walkDir = void 0;
 /* eslint-disable no-await-in-loop */
 /* eslint-disable no-restricted-syntax */
 const fs_1 = __importDefault(require("fs"));
@@ -22,6 +21,7 @@ async function walkDir(dir, callback) {
         }
     }
 }
+exports.walkDir = walkDir;
 function walkDirSync(dir, callback) {
     const subDirs = fs_1.default.readdirSync(dir);
     for (const subDir of subDirs) {
@@ -35,3 +35,4 @@ function walkDirSync(dir, callback) {
         }
     }
 }
+exports.walkDirSync = walkDirSync;

package/example/material.json

@@ -90,5 +90,11 @@
     "schemaVersion": "0.2.0",
     "slug": "silicon-fcc",
     "unitCellFormula": "Si2",
-    "updatedAt": "2016-04-04T17:58:42.867Z"
+    "updatedAt": "2016-04-04T17:58:42.867Z",
+    "metadata": {
+        "boundaryConditions": {
+            "type": "pbc",
+            "offset": 0.0
+        }
+    }
 }

package/example/model.json

@@ -3,5 +3,6 @@
         "...": "include(method.json)"
     },
     "subtype": "gga",
-    "type": "dft"
+    "type": "dft",
+    "functional": "pbe"
 }

package/example/software/application.json

@@ -2,6 +2,7 @@
     "name": "espresso",
     "shortName": "qe",
     "summary": "Quantum Espresso",
+    "build": "GNU",
     "version": "6.3",
     "hasAdvancedComputeOptions": true,
     "isUsingMaterial": true

package/example/software/executable.json

@@ -1,15 +1,14 @@
 {
+    "name": "pw.x",
+    "applicationName": "pw.x",
+    "applicationVersion": "7.0",
     "advancedComputeOptions": true,
-    "applicationId": [
-        "eaJepm4AWfqpaCw59"
-    ],
     "isDefault": true,
     "monitors": [
         {
             "name": "standard_output"
         }
     ],
-    "name": "pw.x",
     "postProcessors": [],
     "preProcessors": [],
     "results": [

package/example/software/flavor.json

@@ -1,9 +1,16 @@
 {
-    "executableId": "4987JFJ3kKbwvFSG7",
+    "name": "pw_scf",
+    "executableName": "pw.x",
+    "applicationName": "pw.x",
+    "applicationVersion": "7.0",
     "input": [
         {
+            "name": "in.scf",
             "templateId": "dJ7HYz5pQ4AuN5qc9"
         }
     ],
-    "name": "pw_scf"
+    "postProcessors": [],
+    "preProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/software/template.json

@@ -1,15 +1,12 @@
 {
-    "applicationName": "espresso",
-    "applicationVersions": [
-        "6.0"
-    ],
+    "name": "kpoints_grid",
+    "executableName": "pw.x",
+    "applicationName": "pw.x",
+    "applicationVersion": "7.0",
     "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
-    "rendered": "K_POINTS automatic\n10 10 10 0 0 0",
     "contextProviders": [
         {
             "name": "KGridManagerMixin"
         }
-    ],
-    "executableName": "pw.x",
-    "name": "kpoints_grid"
+    ]
 }

package/example/software_directory/modeling/espresso.json

@@ -2,5 +2,6 @@
     "name": "espresso",
     "shortName": "qe",
     "summary": "Quantum Espresso",
-    "version": "7.2"
+    "version": "7.2",
+    "build": "GNU"
 }

package/example/software_directory/modeling/nwchem.json

@@ -1,6 +1,8 @@
 {
     "name": "NWChem",
     "summary": "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations",
+    "shortName": "nwchem",
     "version": "6.6",
-    "exec": "nwchem"
-} 
+    "exec": "nwchem",
+    "build": "GNU"
+}

package/example/software_directory/modeling/unit/execution.json

@@ -6,10 +6,25 @@
     "head": true,
     "input": [
         {
-            "...": "include(../../../software/template.json)"
+            "template": {
+                "...": "include(../../../software/template.json)"
+            },
+            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+            "isManuallyChanged": false
         }
     ],
     "name": "modeling",
     "status": "idle",
-    "type": "execution"
+    "type": "execution",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": [],
+    "context": [],
+    "executable": {
+        "...": "include(../../../software/executable.json)"
+    },
+    "flavor": {
+        "...": "include(../../../software/flavor.json)"
+    }
 }

package/example/software_directory/modeling/vasp.json

@@ -2,5 +2,6 @@
     "name": "vasp",
     "shortName": "vasp",
     "summary": "vienna ab-initio simulation package",
-    "version": "5.3.5"
+    "version": "5.3.5",
+    "build": "GNU"
 }

package/example/software_directory/scripting/jupyter-lab.json

@@ -4,5 +4,6 @@
     "name": "jupyterLab",
     "shortName": "jl",
     "summary": "Jupyter Lab",
-    "version": "0.33.12"
+    "version": "0.33.12",
+    "build": "GNU"
 }

package/example/software_directory/scripting/python.json

@@ -4,5 +4,6 @@
     "name": "python",
     "shortName": "py",
     "summary": "Python Script",
-    "version": "2.7.5"
+    "version": "2.7.5",
+    "build": "GNU"
 }

package/example/software_directory/scripting/shell.json

@@ -4,5 +4,6 @@
     "name": "shell",
     "shortName": "sh",
     "summary": "Shell Script",
-    "version": "4.2.46"
+    "version": "4.2.46",
+    "build": "GNU"
 }

package/example/software_directory/scripting/unit/execution.json

@@ -7,10 +7,25 @@
     "head": true,
     "input": [
         {
-            "...": "include(../../../software/template.json)"
+            "template": {
+                "...": "include(../../../software/template.json)"
+            },
+            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+            "isManuallyChanged": false
         }
     ],
     "name": "scripting",
     "status": "idle",
-    "type": "execution"
+    "type": "execution",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": [],
+    "executable": {
+        "...": "include(../../../software/executable.json)"
+    },
+    "flavor": {
+        "...": "include(../../../software/flavor.json)"
+    },
+    "context": []
 }

package/example/system/runtime_items.json

@@ -0,0 +1,14 @@
+{
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [
+        {
+            "name": "standard_output"
+        }
+    ],
+    "results": [
+        {
+            "name": "atomic_forces"
+        }
+    ]
+}

package/example/workflow/unit/assignment.json

@@ -15,5 +15,9 @@
     "operand": "N_K_x",
     "status": "idle",
     "type": "assignment",
-    "value": "N_K_x+N_K_y+1"
+    "value": "N_K_x+N_K_y+1",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/workflow/unit/condition.json

@@ -18,5 +18,9 @@
     "status": "idle",
     "then": "sample_id_4",
     "throwException": true,
-    "type": "condition"
+    "type": "condition",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/workflow/unit/execution.json

@@ -13,8 +13,11 @@
     "head": true,
     "input": [
         {
-            "content": "K_POINTS automatic\n2 2 2 0 0 0",
-            "name": "pw_scf.in"
+            "template": {
+                "...": "include(../../software/template.json)"
+            },
+            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+            "isManuallyChanged": false
         }
     ],
     "monitors": [
@@ -35,5 +38,6 @@
         }
     ],
     "status": "idle",
-    "type": "execution"
+    "type": "execution",
+    "context": []
 }

package/example/workflow/unit/io/api.json

@@ -1,4 +1,5 @@
 {
+    "type": "api",
     "endpoint": "data-frame",
     "endpoint_options": {
         "data": {

package/example/workflow/unit/io/db_collection.json

@@ -0,0 +1,5 @@
+{
+    "collection": "features",
+    "draft": false,
+    "type": "db_collection"
+}

package/example/workflow/unit/io/db_ids.json

@@ -0,0 +1,6 @@
+{
+    "ids": [
+        "KuAsBRwofzGfHPWiT"
+    ],
+    "type": "db_ids"
+}

package/example/workflow/unit/io/object_storage.json

@@ -4,5 +4,6 @@
     "objectData": {
         "...": "include(../../../core/reusable/object_storage_container_data.json)"
     },
-    "filetype": "text/html"
+    "filetype": "text/html",
+    "type": "object_storage"
 }

package/example/workflow/unit/io.json

@@ -3,39 +3,19 @@
     "head": true,
     "input": [
         {
-            "endpoint": "data-frame",
-            "endpoint_options": {
-                "data": {
-                    "features": [
-                        "elemental_ratio:Si",
-                        "elemental_ratio:Ge",
-                        "ionization_potential:Ge",
-                        "ionization_potential:Si"
-                    ],
-                    "ids": [
-                        "KuAsBRwofzGfHPWiT"
-                    ],
-                    "targets": [
-                        "band_gaps:indirect",
-                        "band_gaps:direct"
-                    ]
-                },
-                "headers": {
-                    "X-Auth-Token": "",
-                    "X-User-Id": ""
-                },
-                "method": "POST",
-                "params": {
-                    "query": {
-                        "formula": "SiGe"
-                    }
-                }
-            }
+            "...": "include(./io/object_storage.json)"
+        },
+        {
+            "...": "include(./io/api.json)"
         }
     ],
     "name": "io",
     "source": "api",
     "status": "idle",
     "subtype": "input",
-    "type": "io"
+    "type": "io",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/workflow/unit/map.json

@@ -12,5 +12,9 @@
     "name": "map",
     "status": "idle",
     "type": "map",
-    "workflowId": "zxjhEiaQvwWwvB3oM"
+    "workflowId": "zxjhEiaQvwWwvB3oM",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/workflow/unit/reduce.json

@@ -12,5 +12,9 @@
     "mapFlowchartId": "1",
     "name": "reduce",
     "status": "idle",
-    "type": "reduce"
+    "type": "reduce",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

package/example/workflow.json

@@ -21,6 +21,7 @@
             "...": "include(workflow/subworkflow.json)"
         }
     ],
+    "workflows": [],
     "tags": [
         "workflow"
     ],
@@ -29,7 +30,11 @@
             "_id": "LCthJ6E2QabYCZqf4",
             "flowchartId": "05c362dc27ff1bb98d16fd60",
             "type": "subworkflow",
-            "name": "subworkflow unit"
+            "name": "subworkflow unit",
+            "preProcessors": [],
+            "postProcessors": [],
+            "monitors": [],
+            "results": []
         }
     ]
 }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2026.5.18-2",
+    "version": "2026.5.27-0",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
         "transpile": "tsc -p tsconfig-transpile.json",
@@ -98,6 +98,7 @@
         "./dist/js/example/*": "./dist/js/example/*",
         "./dist/js/utils/*": "./dist/js/utils/*.js",
         "./dist/js/esse/*": "./dist/js/esse/*.js",
+        "./dist/js/esse/server/*": "./dist/js/esse/server/*.js",
         "./dist/js/json_include/*": "./dist/js/json_include/*.js",
         "./dist/js/scripts/*": "./dist/js/scripts/*.js",
         "./dist/js/types": "./dist/js/types.js",

package/schema/apse/file/applications/espresso/7.2/pw.x/atomic_species.json

@@ -23,7 +23,12 @@
                         "type": "string",
                         "description": "PseudoPot_X"
                     }
-                }
+                },
+                "required": [
+                    "X",
+                    "Mass_X",
+                    "PseudoPot_X"
+                ]
             }
         }
     }

package/schema/context_providers_directory/by_application/nwchem_total_energy_context_provider.json

@@ -5,6 +5,11 @@
     "description": "Schema for NWChemTotalEnergyContextProvider that generates context data for NWChem total energy input.",
     "type": "object",
     "properties": {
+        "contextProviderName": {
+            "type": "string",
+            "const": "nwchem-total-energy",
+            "description": "Descriminator for AJV validator"
+        },
         "CHARGE": {
             "type": "integer",
             "description": "Total charge of the system."
@@ -56,7 +61,8 @@
         "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS",
         "ATOMIC_SPECIES",
         "FUNCTIONAL",
-        "CARTESIAN"
+        "CARTESIAN",
+        "contextProviderName"
     ]
 }
 

package/schema/context_providers_directory/by_application/qe_neb_context_provider.json

@@ -11,19 +11,24 @@
             "type": "object",
             "properties": {
                 "FIRST_IMAGE": {
-                    "type": "string",
-                    "description": "Atomic positions block (ATOMIC_POSITIONS) for the first NEB image."
+                    "description": "Atomic positions block (ATOMIC_POSITIONS) for the first NEB image.",
+                    "$ref": "../../apse/file/applications/espresso/7.2/pw.x/atomic_positions.json#/properties/values"
                 },
                 "LAST_IMAGE": {
-                    "type": "string",
-                    "description": "Atomic positions block (ATOMIC_POSITIONS) for the last NEB image."
+                    "description": "Atomic positions block (ATOMIC_POSITIONS) for the last NEB image.",
+                    "$ref": "../../apse/file/applications/espresso/7.2/pw.x/atomic_positions.json#/properties/values"
                 },
                 "INTERMEDIATE_IMAGES": {
                     "type": "array",
                     "description": "Atomic positions blocks (ATOMIC_POSITIONS) for all intermediate NEB images.",
                     "items": {
-                        "type": "string"
+                        "$ref": "../../apse/file/applications/espresso/7.2/pw.x/atomic_positions.json#/properties/values"
                     }
+                },
+                "contextProviderName": {
+                    "type": "string",
+                    "const": "qe-neb",
+                    "description": "Descriminator for AJV validator"
                 }
             },
             "required": [
@@ -37,7 +42,8 @@
                 "CELL_PARAMETERS",
                 "FIRST_IMAGE",
                 "LAST_IMAGE",
-                "INTERMEDIATE_IMAGES"
+                "INTERMEDIATE_IMAGES",
+                "contextProviderName"
             ]
         }
     ]

package/schema/context_providers_directory/by_application/qe_pwx_context_provider.json

@@ -9,6 +9,13 @@
         },
         {
             "type": "object",
+            "properties": {
+                "contextProviderName": {
+                    "type": "string",
+                    "const": "qe-pwx",
+                    "description": "Descriminator for AJV validator"
+                }
+            },
             "required": [
                 "IBRAV",
                 "RESTART_MODE",
@@ -19,8 +26,10 @@
                 "NTYP_WITH_LABELS",
                 "ATOMIC_POSITIONS",
                 "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS",
-                "CELL_PARAMETERS"
+                "CELL_PARAMETERS",
+                "contextProviderName"
             ]
         }
     ]
+    
 }