@mat3ra/esse 2023.12.25-2

package/example/software_directory/ml/unit/execution/train.json

@@ -0,0 +1,26 @@
+{
+    "application": {
+        "...": "include(../../exabyteml.json)"
+    },
+    "flavor": {
+        "executableId": "4987JFJ3kKbwvFSG7",
+        "name": "train"
+    },
+    "flowchartId": "train",
+    "head": true,
+    "input": {
+        "features": [
+            "elemental_ratio:Si",
+            "elemental_ratio:Ge",
+            "ionization_potential:Ge",
+            "ionization_potential:Si"
+        ],
+        "targets": [
+            "band_gaps:indirect",
+            "band_gaps:direct"
+        ]
+    },
+    "name": "train",
+    "status": "idle",
+    "type": "execution"
+}

package/example/software_directory/ml/unit/processing/data_transformation/manipulation.json

@@ -0,0 +1,14 @@
+{
+    "flowchartId": "data_transformation",
+    "head": true,
+    "inputData": {
+        "cleanMissingData": true,
+        "removeDuplicateRows": true,
+        "replaceNoneValuesWith": 0
+    },
+    "name": "data_transformation",
+    "operation": "data_transformation",
+    "operationType": "manipulation",
+    "status": "idle",
+    "type": "processing"
+}

package/example/software_directory/ml/unit/processing/data_transformation/scale_and_reduce.json

@@ -0,0 +1,26 @@
+{
+    "flowchartId": "data_transformation",
+    "head": true,
+    "inputData": {
+        "perFeature": [
+            {
+                "mean": 0.156,
+                "name": "atomic_radius:Ge",
+                "scale": 1.5,
+                "variance": 0.1
+            },
+            {
+                "mean": 0.155,
+                "name": "atomic_radius:Si",
+                "scale": 1.4,
+                "variance": 0.11
+            }
+        ],
+        "scaler": "standard_scaler"
+    },
+    "name": "data_transformation",
+    "operation": "data_transformation",
+    "operationType": "scale_and_reduce",
+    "status": "idle",
+    "type": "processing"
+}

package/example/software_directory/ml/unit/processing/feature_selection/filter_based.json

@@ -0,0 +1,13 @@
+{
+    "flowchartId": "feature_selection",
+    "head": true,
+    "inputData": {
+        "algorithm": "f_regression",
+        "nFeatures": 100
+    },
+    "name": "feature_selection",
+    "operation": "feature_selection",
+    "operationType": "filter_based",
+    "status": "idle",
+    "type": "processing"
+}

package/example/software_directory/modeling/espresso/arguments.json

@@ -0,0 +1,5 @@
+{
+    "nband": 1,
+    "npools": 1,
+    "ntg": 1
+}

package/example/software_directory/modeling/espresso.json

@@ -0,0 +1,6 @@
+{
+    "name": "espresso",
+    "shortName": "qe",
+    "summary": "Quantum Espresso",
+    "version": "5.1.1"
+}

package/example/software_directory/modeling/nwchem.json

@@ -0,0 +1,6 @@
+{
+    "name": "NWChem",
+    "summary": "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations",
+    "version": "6.6",
+    "exec": "nwchem"
+} 

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

@@ -0,0 +1,16 @@
+{
+    "application": {
+        "...": "include(../espresso.json)"
+    },
+    "flowchartId": "modeling",
+    "head": true,
+    "input": [
+        {
+            "content": "K_POINTS automatic\n2 2 2 0 0 0",
+            "name": "pw_scf.in"
+        }
+    ],
+    "name": "modeling",
+    "status": "idle",
+    "type": "execution"
+}

package/example/software_directory/modeling/vasp.json

@@ -0,0 +1,6 @@
+{
+    "name": "vasp",
+    "shortName": "vasp",
+    "summary": "vienna ab-initio simulation package",
+    "version": "5.3.5"
+}

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

@@ -0,0 +1,8 @@
+{
+    "exec": "jupyter",
+    "flavor": "notebook",
+    "name": "jupyterLab",
+    "shortName": "jl",
+    "summary": "Jupyter Lab",
+    "version": "0.33.12"
+}

package/example/software_directory/scripting/python.json

@@ -0,0 +1,8 @@
+{
+    "exec": "python",
+    "flavor": "python2",
+    "name": "python",
+    "shortName": "py",
+    "summary": "Python Script",
+    "version": "2.7.5"
+}

package/example/software_directory/scripting/shell.json

@@ -0,0 +1,8 @@
+{
+    "exec": "sh",
+    "flavor": "sh",
+    "name": "shell",
+    "shortName": "sh",
+    "summary": "Shell Script",
+    "version": "4.2.46"
+}

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

@@ -0,0 +1,17 @@
+{
+    "application": {
+        "...": "include(../python.json)"
+    },
+    "compute": null,
+    "flowchartId": "scripting",
+    "head": true,
+    "input": [
+        {
+            "content": "print('Hello World!')",
+            "name": "script.py"
+        }
+    ],
+    "name": "scripting",
+    "status": "idle",
+    "type": "execution"
+}

package/example/system/_material.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Material",
+    "slug": "silicon-fcc"
+}

package/example/system/_parent_job.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Job",
+    "slug": "parent-job"
+}

package/example/system/_project.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Project",
+    "slug": "project-default"
+}

package/example/system/consistency_check.json

@@ -0,0 +1,6 @@
+{
+    "key": "basis.coordinates.0",
+    "name": "atomsTooClose",
+    "severity": "warning",
+    "message": "Atom 0 is too close to atom X"
+}

package/example/system/creator.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "User",
+    "slug": "exadmin"
+}

package/example/system/entity_reference.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Class",
+    "slug": "Slug"
+}

package/example/system/file_source.json

@@ -0,0 +1,6 @@
+{
+    "extension": "poscar",
+    "filename": "POSCAR.mp-546794_SiO2.poscar",
+    "text": "Si4 O8\n1.0\n5.073173 0.000000 0.000000\n0.000000 5.073173 0.000000\n0.000000 0.000000 7.359653\nSi O\n4 8\ndirect\n0.000000 0.500000 0.250000 Si\n0.500000 0.500000 0.500000 Si\n0.500000 0.000000 0.750000 Si\n0.000000 0.000000 0.000000 Si\n0.750000 0.584672 0.375000 O\n0.915328 0.250000 0.125000 O\n0.084672 0.750000 0.125000 O\n0.250000 0.415328 0.375000 O\n0.250000 0.084672 0.875000 O\n0.415328 0.750000 0.625000 O\n0.584672 0.250000 0.625000 O\n0.750000 0.915328 0.875000 O",
+    "hash": "fce4c03798763a9ed8bf64d762c7fbfd"
+}

package/example/system/message.json

@@ -0,0 +1,14 @@
+{
+    "header": {
+        "entity": {
+            "_id": "FPjAaKfuYAL7tiHbm",
+            "flowchartId": "pw_scf",
+            "name": "unit"
+        },
+        "timestamp": 1234923492.12,
+        "version": "0.2.0"
+    },
+    "payload": {
+        "...": "include(../properties_directory/scalar/total_energy.json)"
+    }
+}

package/example/system/owner.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Account",
+    "slug": "exabyte"
+}

package/example/workflow/subworkflow.json

@@ -0,0 +1,18 @@
+{
+    "_id": "LCthJ6E2QabYCZqf4",
+    "application": {
+        "...": "include(../software/application.json)"
+    },
+    "model": {
+        "...": "include(../model.json)"
+    },
+    "name": "Band Structure",
+    "properties": [
+        "band_structure"
+    ],
+    "units": [
+        {
+            "...": "include(unit.json)"
+        }
+    ]
+}

package/example/workflow/unit/assignment.json

@@ -0,0 +1,19 @@
+{
+    "flowchartId": "assignment",
+    "head": true,
+    "input": [
+        {
+            "name": "N_K_x",
+            "scope": "global"
+        },
+        {
+            "name": "N_K_y",
+            "scope": "global"
+        }
+    ],
+    "name": "assignment",
+    "operand": "N_K_x",
+    "status": "idle",
+    "type": "assignment",
+    "value": "N_K_x+N_K_y+1"
+}

package/example/workflow/unit/condition.json

@@ -0,0 +1,22 @@
+{
+    "else": "sample_id_6",
+    "flowchartId": "condition",
+    "head": true,
+    "input": [
+        {
+            "name": "x",
+            "scope": "global"
+        },
+        {
+            "name": "total_energy",
+            "scope": "sample_id_2"
+        }
+    ],
+    "maxOccurrences": 100,
+    "name": "condition",
+    "statement": "abs(x-total_energy) < 1e-5",
+    "status": "idle",
+    "then": "sample_id_4",
+    "throwException": true,
+    "type": "condition"
+}

package/example/workflow/unit/execution.json

@@ -0,0 +1,39 @@
+{
+    "application": {
+        "...": "include(../../software/application.json)"
+    },
+    "compute": null,
+    "executable": {
+        "...": "include(../../software/executable.json)"
+    },
+    "flavor": {
+        "...": "include(../../software/flavor.json)"
+    },
+    "flowchartId": "execution",
+    "head": true,
+    "input": [
+        {
+            "content": "K_POINTS automatic\n2 2 2 0 0 0",
+            "name": "pw_scf.in"
+        }
+    ],
+    "monitors": [
+        {
+            "name": "scf_accuracy"
+        },
+        {
+            "name": "standard_output"
+        }
+    ],
+    "name": "execution",
+    "next": "pw-bands",
+    "postProcessors": [],
+    "preProcessors": [],
+    "results": [
+        {
+            "name": "harris_foulkes_estimate"
+        }
+    ],
+    "status": "idle",
+    "type": "execution"
+}

package/example/workflow/unit/input/_inputItemScope.json

@@ -0,0 +1,4 @@
+{
+    "name": "N_K_y",
+    "scope": "global"
+}

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

@@ -0,0 +1,31 @@
+{
+    "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"
+            }
+        }
+    },
+    "name": "DATA"
+}

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

@@ -0,0 +1,15 @@
+{
+    "features": [
+        "elemental_ratio:Si",
+        "elemental_ratio:Ge",
+        "ionization_potential:Ge",
+        "ionization_potential:Si"
+    ],
+    "ids": [
+        "KuAsBRwofzGfHPWiT"
+    ],
+    "targets": [
+        "band_gaps:indirect",
+        "band_gaps:direct"
+    ]
+}

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

@@ -0,0 +1,7 @@
+{
+    "basename": "index.html",
+    "overwrite": true,
+    "objectData": {
+        "...": "include(../../../core/reusable/object_storage_container_data.json)"
+    }
+}

package/example/workflow/unit/io.json

@@ -0,0 +1,41 @@
+{
+    "flowchartId": "io",
+    "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"
+                    }
+                }
+            }
+        }
+    ],
+    "name": "io",
+    "source": "api",
+    "status": "idle",
+    "subtype": "input",
+    "type": "io"
+}

package/example/workflow/unit/map.json

@@ -0,0 +1,16 @@
+{
+    "flowchartId": "map",
+    "head": true,
+    "input": {
+        "target": "MAP_K_POINTS_1",
+        "values": [
+            "2 2 2 0 0 0",
+            "3 3 3 0 0 0",
+            "4 4 4 0 0 0"
+        ]
+    },
+    "name": "map",
+    "status": "idle",
+    "type": "map",
+    "workflowId": "zxjhEiaQvwWwvB3oM"
+}

package/example/workflow/unit/processing.json

@@ -0,0 +1,13 @@
+{
+    "flowchartId": "data_transformation_manipulation",
+    "inputData": {
+        "cleanMissingData": true,
+        "removeDuplicateRows": true,
+        "replaceNoneValuesWith": 0
+    },
+    "name": "data_transformation_manipulation",
+    "operation": "data_transformation",
+    "operationType": "manipulation",
+    "status": "idle",
+    "type": "processing"
+}

package/example/workflow/unit/reduce.json

@@ -0,0 +1,16 @@
+{
+    "flowchartId": "reduce",
+    "head": true,
+    "input": [
+        {
+            "arguments": [
+                "band_gaps"
+            ],
+            "operation": "aggregate"
+        }
+    ],
+    "mapFlowchartId": "1",
+    "name": "reduce",
+    "status": "idle",
+    "type": "reduce"
+}

package/example/workflow/unit/runtime/runtime_items.json

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

package/example/workflow/unit.json

@@ -0,0 +1,8 @@
+{
+    "flowchartId": "pw-scf",
+    "head": true,
+    "name": "pw_scf",
+    "status": "idle",
+    "type": "execution",
+    "tags": ["test-tags"]
+}

package/example/workflow.json

@@ -0,0 +1,34 @@
+{
+    "_id": "FPjAaKfuYAL7tiHbm",
+    "createdAt": "2018-11-19 06:41:46.877Z",
+    "creator": {
+        "...": "include(system/creator.json)"
+    },
+    "exabyteId": "qKtTzu9utCo6ac4n7",
+    "hash": "f4fd707d2e47c15f8d786cf159040954",
+    "isDefault": true,
+    "name": "workflow",
+    "owner": {
+        "...": "include(system/owner.json)"
+    },
+    "properties": [
+        "band_structure"
+    ],
+    "schemaVersion": "0.2.0",
+    "slug": "workflow",
+    "subworkflows": [
+        {
+            "...": "include(workflow/subworkflow.json)"
+        }
+    ],
+    "tags": [
+        "workflow"
+    ],
+    "units": [
+        {
+            "_id": "LCthJ6E2QabYCZqf4",
+            "flowchartId": "05c362dc27ff1bb98d16fd60",
+            "type": "subworkflow"
+        }
+    ]
+}

package/lib/js/esse/index.js

@@ -0,0 +1,83 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.ESSE = void 0;
+
+var _ajv = _interopRequireDefault(require("ajv"));
+
+var _schemaUtils = require("./schemaUtils");
+
+var _settings = require("./settings");
+
+var _utils = require("./utils");
+
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }
+
+function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, "prototype", { writable: false }); return Constructor; }
+
+function _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }
+
+var SCHEMAS = (0, _utils.parseIncludeReferenceStatementsByDir)(_settings.SCHEMAS_DIR);
+var EXAMPLES = (0, _utils.parseIncludeReferenceStatementsByDir)(_settings.EXAMPLES_DIR, true);
+
+var ESSE = /*#__PURE__*/function () {
+  function ESSE() {
+    _classCallCheck(this, ESSE);
+
+    _defineProperty(this, "validate", function (example, schema) {
+      var ajv = new _ajv["default"]({
+        allErrors: true
+      });
+      var isValid = ajv.validate(schema, example);
+
+      if (!isValid) {
+        console.error(ajv.errors);
+      }
+
+      return isValid;
+    });
+
+    this.schemas = SCHEMAS;
+    this.wrappedExamples = EXAMPLES;
+    this.examples = EXAMPLES.map(function (example) {
+      return example.data;
+    });
+  }
+
+  _createClass(ESSE, [{
+    key: "getSchemaById",
+    value: function getSchemaById(schemaId) {
+      return this.schemas.find(function (schema) {
+        return schema.$id === schemaId;
+      });
+    }
+    /**
+     * Validates a given example against the schema.
+     * @param example {Object|Array} example to validate.
+     * @param schema {Object} schema to validate the example with.
+     * @returns {boolean} whether example is valid.
+     */
+
+  }, {
+    key: "buildGlobalSchema",
+    value: function buildGlobalSchema() {
+      return {
+        $id: "esse-global-schema",
+        $schema: "http://json-schema.org/draft-04/schema#",
+        title: "Global schema",
+        type: "object",
+        definitions: (0, _schemaUtils.buildSchemaDefinitions)(this.schemas)
+      };
+    }
+  }]);
+
+  return ESSE;
+}();
+
+exports.ESSE = ESSE;