@mat3ra/wode 2026.5.23-0 → 2026.6.5-0

package/dist/js/workflows/create.js

@@ -1,318 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.createWorkflow = createWorkflow;
-var _create = require("../subworkflows/create");
-var _units = require("../units");
-var _map = require("../units/map");
-var _utils = require("../utils");
-var _workflow = require("./workflow");
-/**
- * @summary Helper for creating Map units for complex workflows
- * @param config {Object} map unit configuration
- * @param unitFactoryCls {*} class factory for map unit
- * @returns {*} map unit
- */
-function createMapUnit({
-  config,
-  unitFactoryCls = _units.UnitFactory
-}) {
-  let {
-    input: defaultInput
-  } = _map.defaultMapConfig;
-  if (config.input) {
-    defaultInput = {
-      ...defaultInput,
-      ...config.input
-    };
-  }
-  const unit = unitFactoryCls.create({
-    ..._map.defaultMapConfig,
-    input: defaultInput
-  });
-  return unit;
-}
-
-/**
- * @summary Update subworkflow units with patch configuration defined in the workflow config
- * @param subworkflowData {Object} subworkflow data
- * @param unitConfigs {Array<Object>} array of patch configs for subworkflow units
- * @returns subworkflowData {Object} subworkflowData with patches applied to units
- */
-function updateUnitConfigs({
-  subworkflowData,
-  unitConfigs
-}) {
-  unitConfigs.forEach(config => {
-    const {
-      index,
-      type,
-      config: unitConfig
-    } = config; // unitConfig should contain 'attributes' key
-    const unit = (0, _utils.findUnit)({
-      subworkflowData,
-      index,
-      type
-    });
-    console.log(`  patching ${type} unit ${index} of subworkflow ${subworkflowData.name}`);
-    unit.config = (0, _utils.applyConfig)({
-      obj: unit.config,
-      config: unitConfig
-    });
-    return null;
-  });
-  return subworkflowData;
-}
-
-/**
- * @summary Use subworkflow.createSubworkflow to create a Subworkflow unit
- * @param appName {String} application name
- * @param unitData {*} object containing subworkflow configuration data
- * @param workflowData {*} object containing all workflow configuration data
- * @param swArgs {*} subworkflow classes
- * @returns {*} subworkflow object
- */
-function createSubworkflowUnit({
-  appName,
-  unitData,
-  workflowData,
-  cache,
-  ...swArgs
-}) {
-  const {
-    name: unitName,
-    unitConfigs,
-    config
-  } = unitData;
-  const {
-    subworkflows
-  } = workflowData;
-  const {
-    [appName]: dataByApp
-  } = subworkflows;
-  let {
-    [unitName]: subworkflowData
-  } = dataByApp;
-  subworkflowData.config = {
-    ...subworkflowData.config,
-    ...config
-  };
-  if (unitConfigs) subworkflowData = updateUnitConfigs({
-    subworkflowData,
-    unitConfigs
-  });
-  return (0, _create.createSubworkflow)({
-    subworkflowData,
-    cache,
-    ...swArgs
-  });
-}
-
-/**
- * @summary Create the first workflow object specified in a workflow configuration
- * @param workflow {*|null} the workflow (if already initialized, no-op)
- * @param unit {*} workflow unit object
- * @param type {String} value in ["workflow", "subworkflow"]
- * @param workflowCls {*} workflow class
- * @returns {Workflow|*} workflow object
- */
-function createWorkflowHead({
-  workflow,
-  unit,
-  type,
-  workflowCls
-}) {
-  if (workflow) return workflow;
-  let wf;
-  switch (type) {
-    case "workflow":
-      wf = unit;
-      break;
-    case "subworkflow":
-      wf = workflowCls.fromSubworkflow(unit);
-      break;
-    default:
-      throw new Error(`workflow type=${type} not understood.`);
-  }
-  return wf;
-}
-
-/**
- * @summary Combine workflow units together
- * @param workflow {*} the workflow object
- * @param unit {*} workflow/subworkflow object
- * @param config {*} additional configuration for e.g. map units
- * @param type {String} value in ["workflow", "subworkflow"]
- * @param unitFactoryCls {*} unit factory class for e.g. map units
- * @returns {*} modified workflow
- */
-function composeWorkflow({
-  workflow,
-  unit,
-  config,
-  type,
-  unitFactoryCls
-}) {
-  /* eslint-disable no-case-declarations */
-  switch (type) {
-    case "workflow":
-      const {
-        mapUnit: isMapUnit,
-        ...mapUnitConfig
-      } = config;
-      if (isMapUnit) {
-        const mapUnit = createMapUnit({
-          config: mapUnitConfig,
-          unitFactoryCls
-        });
-        workflow.addMapUnit(mapUnit, unit);
-      } else {
-        console.log("adding workflows directly to workflows is not supported.");
-      }
-      break;
-    case "subworkflow":
-      workflow.addSubworkflow(unit);
-      break;
-    default:
-      throw new Error(`workflow type=${type} not understood.`);
-  }
-  /* eslint-enable no-case-declarations */
-  return workflow;
-}
-
-/**
- * @summary Convert a flattened array of workflow units to a properly constructed workflow
- * @param wfUnits {Array} array of workflow units
- * @param workflowCls {*} workflow class
- * @param unitFactoryCls {*} unit factory class
- * @returns {*} constructed workflow
- */
-function createFromWorkflowUnits({
-  wfUnits,
-  workflowCls,
-  unitFactoryCls
-}) {
-  let workflow, unit, config, type;
-  wfUnits.map(wfUnit => {
-    ({
-      unit,
-      config,
-      type
-    } = wfUnit);
-    if (!workflow) {
-      workflow = createWorkflowHead({
-        workflow,
-        unit,
-        type,
-        workflowCls
-      });
-    } else {
-      workflow = composeWorkflow({
-        workflow,
-        unit,
-        config,
-        type,
-        unitFactoryCls
-      });
-    }
-    return null;
-  });
-  return (0, _utils.applyConfig)({
-    obj: workflow,
-    config
-  });
-}
-
-/**
- * @summary Creates a flattened array of workflow units from nested workflow/subworkflow
- * configuration data comprising a simple or complex workflow
- * @param appName
- * @param units
- * @param swArgs
- * @returns {*[]}
- */
-function createWorkflowUnits({
-  appName,
-  workflowData,
-  workflowSubworkflowMapByApplication,
-  workflowCls,
-  cache = [],
-  ...swArgs
-}) {
-  const wfUnits = [];
-  const {
-    units
-  } = workflowData;
-  let unit, config;
-  units.map(unitData => {
-    const {
-      type
-    } = unitData;
-    switch (type) {
-      case "workflow":
-        ({
-          config
-        } = unitData);
-        unit = createWorkflowUnits({
-          appName,
-          workflowData: unitData,
-          workflowSubworkflowMapByApplication,
-          workflowCls,
-          ...swArgs
-        });
-        break;
-      case "subworkflow":
-        ({
-          config
-        } = workflowData);
-        unit = createSubworkflowUnit({
-          appName,
-          unitData,
-          workflowData: workflowSubworkflowMapByApplication,
-          cache,
-          ...swArgs
-        });
-        break;
-      default:
-        break;
-    }
-    wfUnits.push({
-      config,
-      unit,
-      type
-    });
-    return null;
-  });
-  return createFromWorkflowUnits({
-    wfUnits,
-    workflowCls,
-    subworkflowCls: swArgs.subworkflowCls,
-    unitFactoryCls: swArgs.unitFactoryCls
-  });
-}
-function createWorkflow({
-  appName,
-  workflowData,
-  workflowSubworkflowMapByApplication,
-  workflowCls = _workflow.Workflow,
-  ...swArgs
-}) {
-  const cache = [];
-  const {
-    name
-  } = workflowData;
-  console.log(`wode: creating ${appName} workflow ${name}`);
-  const wf = createWorkflowUnits({
-    appName,
-    workflowData,
-    workflowSubworkflowMapByApplication,
-    workflowCls,
-    cache,
-    ...swArgs
-  });
-  wf.setName(name);
-  wf.applicationName = appName;
-  return wf;
-}

package/dist/js/workflows/index.js

@@ -1,113 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "Workflow", {
-  enumerable: true,
-  get: function () {
-    return _workflow.Workflow;
-  }
-});
-Object.defineProperty(exports, "createWorkflow", {
-  enumerable: true,
-  get: function () {
-    return _create.createWorkflow;
-  }
-});
-exports.createWorkflowConfigs = createWorkflowConfigs;
-exports.createWorkflows = createWorkflows;
-var _ade = require("@mat3ra/ade");
-var _JSONSchemasInterface = _interopRequireDefault(require("@mat3ra/esse/dist/js/esse/JSONSchemasInterface"));
-var _schemas = _interopRequireDefault(require("@mat3ra/esse/dist/js/schemas.json"));
-var _patch = require("../patch");
-var _create = require("./create");
-var _workflow = require("./workflow");
-function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-// Import Template here to apply context provider patch
-// eslint-disable-next-line no-unused-vars
-
-// Running this to set schemas for validation, removing the redundant data from application-flavors tree: `flavors`
-_JSONSchemasInterface.default.setSchemas(_schemas.default);
-
-/*
-    Workflow construction follows these rules:
-        1. Workflow is constructed as a collection of subworkflows defined in JSON
-        2. A "units" key should contain at least one object referencing the workflow itself
-        3. Additional workflows are added in order specified in the same "units" array
-        4. map units are added along with their workflows according to data in "units"
-        5. top-level subworkflows are added directly in the order also specified by "units"
- */
-function createWorkflows({
-  appName = null,
-  workflowCls = _workflow.Workflow,
-  workflowSubworkflowMapByApplication,
-  ...swArgs
-}) {
-  let apps = appName !== null ? [appName] : _ade.allApplications;
-  const allApplicationsFromWorkflowData = Object.keys(workflowSubworkflowMapByApplication.workflows);
-  // output warning if allApplications and allApplicationsFromWorkflowData do not match
-  if (appName === null) {
-    if (apps && apps.sort().join(",") !== allApplicationsFromWorkflowData.sort().join(",")) {
-      // eslint-disable-next-line no-console
-      console.warn(`Warning: allApplications and allApplicationsFromWorkflowData do not match:
-                ${apps.sort().join(",")} !== ${allApplicationsFromWorkflowData.sort().join(",")}`);
-      console.warn("Using allApplicationsFromWorkflowData");
-    }
-    apps = allApplicationsFromWorkflowData;
-  }
-  const wfs = [];
-  const {
-    workflows
-  } = workflowSubworkflowMapByApplication;
-  apps.map(name => {
-    const {
-      [name]: dataByApp
-    } = workflows;
-    Object.values(dataByApp).map(workflowDataForApp => {
-      wfs.push((0, _create.createWorkflow)({
-        appName: name,
-        workflowData: workflowDataForApp,
-        workflowSubworkflowMapByApplication,
-        workflowCls,
-        ...swArgs
-      }));
-      return null;
-    });
-    return null;
-  });
-  return wfs;
-}
-
-/**
- * @summary Create workflow configurations for all applications
- * @param applications {Array<String>} array of application names
- * @param workflowCls {*} workflow class to instantiate
- * @param workflowSubworkflowMapByApplication {Object} object containing all workflow/subworkflow map by application
- * @param swArgs {Object} other classes for instantiation
- * @returns {Array<Object>} array of workflow configurations
- */
-function createWorkflowConfigs({
-  applications,
-  workflowCls = _workflow.Workflow,
-  workflowSubworkflowMapByApplication,
-  ...swArgs
-}) {
-  const configs = [];
-  applications.forEach(app => {
-    const workflows = createWorkflows({
-      appName: app,
-      workflowCls,
-      workflowSubworkflowMapByApplication,
-      ...swArgs
-    });
-    workflows.forEach(wf => {
-      configs.push({
-        application: app,
-        name: wf.prop("name"),
-        config: wf.toJSON()
-      });
-    });
-  });
-  return configs;
-}

package/dist/js/workflows/relaxation.js

@@ -1,38 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.RelaxationLogicMixin = void 0;
-var _standata = require("@mat3ra/standata");
-const RelaxationLogicMixin = superclass => class extends superclass {
-  get relaxationSubworkflow() {
-    const appName = this.subworkflows[0]?.application?.name;
-    if (!appName) return undefined;
-    const subworkflowStandata = new _standata.SubworkflowStandata();
-    const relaxationSubworkflow = subworkflowStandata.getRelaxationSubworkflowByApplication(appName);
-    if (!relaxationSubworkflow) return undefined;
-    return new this._Subworkflow(relaxationSubworkflow);
-  }
-  isRelaxationSubworkflow(subworkflow) {
-    const {
-      relaxationSubworkflow
-    } = this;
-    return relaxationSubworkflow?.systemName !== undefined && relaxationSubworkflow.systemName === subworkflow.systemName;
-  }
-  get hasRelaxation() {
-    return this.subworkflows.some(subworkflow => this.isRelaxationSubworkflow(subworkflow));
-  }
-  toggleRelaxation() {
-    if (this.hasRelaxation) {
-      const relaxSubworkflow = this.subworkflows.find(sw => this.isRelaxationSubworkflow(sw));
-      this.removeSubworkflow(relaxSubworkflow.id);
-    } else {
-      const vcRelax = this.relaxationSubworkflow;
-      if (vcRelax) {
-        this.addSubworkflow(vcRelax, true);
-      }
-    }
-  }
-};
-exports.RelaxationLogicMixin = RelaxationLogicMixin;

package/src/js/context/context.js

@@ -1,47 +0,0 @@
-import { BoundaryConditionsFormDataProvider } from "./providers/BoundaryConditionsFormDataProvider";
-import QENEBContextProvider from "./providers/by_application/espresso/QENEBContextProvider";
-import QEPWXContextProvider from "./providers/by_application/espresso/QEPWXContextProvider";
-import NWChemTotalEnergyContextProvider from "./providers/by_application/nwchem/NWChemTotalEnergyContextProvider";
-import VASPContextProvider from "./providers/by_application/vasp/VASPContextProvider";
-import VASPNEBContextProvider from "./providers/by_application/vasp/VASPNEBContextProvider";
-import { CollinearMagnetizationContextProvider } from "./providers/CollinearMagnetizationContextProvider";
-import { HubbardContextProviderLegacy } from "./providers/HubbardContextProviderLegacy";
-import { HubbardJContextProvider } from "./providers/HubbardJContextProvider";
-import { HubbardUContextProvider } from "./providers/HubbardUContextProvider";
-import { HubbardVContextProvider } from "./providers/HubbardVContextProvider";
-import { IonDynamicsContextProvider } from "./providers/IonDynamicsContextProvider";
-import { MLSettingsContextProvider } from "./providers/MLSettingsContextProvider";
-import { MLTrainTestSplitContextProvider } from "./providers/MLTrainTestSplitContextProvider";
-import { NEBFormDataProvider } from "./providers/NEBFormDataProvider";
-import { NonCollinearMagnetizationContextProvider } from "./providers/NonCollinearMagnetizationContextProvider";
-import { PlanewaveCutoffsContextProvider } from "./providers/PlanewaveCutoffsContextProvider";
-import { PointsGridFormDataProvider } from "./providers/PointsGridFormDataProvider";
-import {
-    ExplicitPointsPath2PIBAFormDataProvider,
-    ExplicitPointsPathFormDataProvider,
-    PointsPathFormDataProvider,
-} from "./providers/PointsPathFormDataProvider";
-
-export default {
-    BoundaryConditionsFormDataProvider,
-    MLSettingsContextProvider,
-    MLTrainTestSplitContextProvider,
-    NEBFormDataProvider,
-    PlanewaveCutoffsContextProvider,
-    PointsGridFormDataProvider,
-    PointsPathFormDataProvider,
-    ExplicitPointsPathFormDataProvider,
-    ExplicitPointsPath2PIBAFormDataProvider,
-    HubbardJContextProvider,
-    HubbardUContextProvider,
-    HubbardVContextProvider,
-    HubbardContextProviderLegacy,
-    IonDynamicsContextProvider,
-    CollinearMagnetizationContextProvider,
-    NonCollinearMagnetizationContextProvider,
-    VASPContextProvider,
-    VASPNEBContextProvider,
-    QEPWXContextProvider,
-    QENEBContextProvider,
-    NWChemTotalEnergyContextProvider,
-};

package/src/js/context/mixins/ApplicationContextMixin.js

@@ -1,19 +0,0 @@
-import { globalSettings } from "../providers/settings";
-
-export function applicationContextMixin(item) {
-    const properties = {
-        _application: undefined,
-
-        initApplicationContextMixin() {
-            this._application =
-                (this.config.context && this.config.context.application) ||
-                globalSettings.Application.createDefault();
-        },
-
-        get application() {
-            return this._application;
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/mixins/JobContextMixin.js

@@ -1,36 +0,0 @@
-const defaultJob = {
-    workflow: {
-        subworkflows: [],
-        units: [],
-    },
-    status: "pre-submission",
-    compute: {
-        queue: "D",
-        nodes: 1,
-        ppn: 1,
-        timeLimit: "3600",
-    },
-    _project: {
-        _id: "",
-    },
-};
-
-export function jobContextMixin(item) {
-    const properties = {
-        isEdited: false,
-
-        _job: defaultJob,
-
-        get job() {
-            return this._job;
-        },
-
-        initJobContextMixin() {
-            const { config } = this;
-            this._job = (config.context && config.context.job) || defaultJob;
-            this.isEdited = false; // we always get the `defaultData` (recalculated from scratch, not persistent)
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/mixins/MaterialContextMixin.js

@@ -1,41 +0,0 @@
-import { globalSettings } from "../providers/settings";
-
-export function materialContextMixin(item) {
-    const properties = {
-        _material: undefined,
-
-        updateMaterialHash() {
-            if (this.isEditedIsSetToFalseOnMaterialUpdate) this.isEdited = false;
-            this.extraData = { materialHash: this.material.hash };
-        },
-
-        // Workaround: Material.createDefault() used to initiate workflow reducer and hence here too
-        //  does not have an id. Here we catch when such material is used and avoid resetting isEdited
-        get isMaterialCreatedDefault() {
-            return !this.material.id;
-        },
-
-        get isMaterialUpdated() {
-            return Boolean(this.extraData && this.extraData.materialHash !== this.material.hash);
-        },
-
-        get material() {
-            if (!this._material) {
-                throw new Error("Material is not set");
-            }
-            return this._material;
-        },
-
-        initMaterialContextMixin() {
-            this._material = this.config.context && this.config.context.material;
-
-            if (!this._material) {
-                this._material = globalSettings.Material.createDefault();
-            }
-
-            this.updateMaterialHash();
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/mixins/MaterialsContextMixin.js

@@ -1,18 +0,0 @@
-import { globalSettings } from "../providers/settings";
-
-export function materialsContextMixin(item) {
-    const properties = {
-        get materials() {
-            return this._materials;
-        },
-        initMaterialsContextMixin() {
-            const materials = this.config.context?.materials;
-            this._materials =
-                materials && materials.length
-                    ? materials
-                    : [globalSettings.Material.createDefault()];
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/mixins/MaterialsSetContextMixin.js

@@ -1,24 +0,0 @@
-import { compareEntitiesInOrderedSetForSorting } from "@mat3ra/code/dist/js/entity/set/ordered/utils";
-
-export function materialsSetContextMixin(item) {
-    const properties = {
-        _materialsSet: undefined,
-
-        get materialsSet() {
-            return this._materialsSet;
-        },
-
-        initMaterialsSetContextMixin() {
-            this._materialsSet = this.config.context?.materialsSet;
-        },
-
-        sortMaterialsByIndexInSet(materials = []) {
-            // DO NOT SORT IN PLACE AS IT CHANGES THE ORDER IN `this.materials` AND HAS SIDE EFFECTS (MaterialViewer).
-            return materials.concat().sort((a, b) => {
-                return compareEntitiesInOrderedSetForSorting(a, b, this.materialsSet._id, false);
-            });
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}