Merge pull request #7 from C-Accel-CRIPT/feat/typescript

feat(scripts): add typescript folder

scripts/typescript/.gitignore

@@ -0,0 +1,3 @@
+node_modules
+build
+out

scripts/typescript/.prettierrc

@@ -0,0 +1,5 @@
+{
+ "tabWidth": 2,
+ "useTabs": false,
+ "printWidth": 120
+}

scripts/typescript/README.md

@@ -0,0 +1,13 @@
+# AFRL transformation script
+
+The purpose of this node script is to convert AFRL dataset to a CRIPT compatible JSON.
+Related to: https://trello.com/c/4eTnhJrp/29-transform-the-afrl-dataset
+
+# `npm i`
+
+Will install this npm package and dependencies.
+
+# Scripts
+
+- `afrl`: see [readme](./src/afrl/README.md)
+- `rcbc`: see [readme](./src/rcbc/README.md)

scripts/typescript/package.json

@@ -0,0 +1,18 @@
+{
+ "name": "cript-typescript",
+ "version": "1.0.0",
+ "description": "Set of typescript code to convert raw data (*.csv, *.ts) to CRIPT *.json format",
+ "main": "index.js",
+ "scripts": {
+ "afrl": "npx ts-node src/afrl/index.ts",
+ "rcbc": "npx ts-node src/rcbc/index.ts",
+ "test": "echo \"Error: no test specified\" && exit 1"
+ },
+ "author": "Bérenger Dalle-Cort, CRIPT, MIT",
+ "license": "MIT",
+ "dependencies": {
+ "csvtojson": "^2.0.10",
+ "ts-node": "^10.9.1",
+ "typescript": "^5.0.3"
+ }
+}

scripts/typescript/src/types/cript/IAlgorithm.ts

@@ -0,0 +1,12 @@
+import { IParameter, ICitation } from '.';
+
+/**
+ * "Algorithm consists of parameter and condition details used in the computation and computational_process. (...)""
+ * @see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=24
+ */
+export type IAlgorithm = {
+ key: string;
+ type: string;
+ parameter: Array<IParameter>;
+ citation: Array<ICitation>;
+};

scripts/typescript/src/types/cript/ICitation.ts

@@ -0,0 +1,22 @@
+import { IReference } from "./IReference";
+
+export type CitationType =
+ 'extracted_by_human' |
+ 'extracted_by_nlp' |
+ 'extracted_by_algorithm' |
+ 'derived_from' |
+ 'replicated' |
+ 'reference';
+
+export interface ICitation {
+ readonly node: ['Citation'];
+
+ name: string;
+ created_at: string;
+ updated_at: string;
+ model_version: string;
+ reference: IReference;
+ uuid: string;
+ // type: string;
+ type: CitationType;
+}

scripts/typescript/src/types/cript/ICollection..ts

@@ -0,0 +1,20 @@
+import { IExperiment, IInventory, IProject } from '.';
+
+export interface ICollection {
+ locked?: boolean;
+ model_version?: string;
+ name: string;
+ notes?: string;
+ readonly node: ['Collection'];
+ public?: boolean;
+ uid?: string;
+ uuid?: string;
+ experiment?: IExperiment[];
+ experiment_count?: number;
+ inventory?: IInventory[];
+ project?: IProject[];
+ inventory_count?: number;
+ created_at?: string;
+ updated_at?: string;
+ doi?: string;
+}

scripts/typescript/src/types/cript/IComputation.ts

@@ -0,0 +1,26 @@
+import { ICondition, IReference, IData, ISoftwareConfiguration, IExperiment, IIngredient, IProperty } from '.';
+
+/**
+ * "The computation node describes the transformation of data or the creation of a computational data set (...)"
+ * @see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=11
+ */
+export interface IComputation {
+ readonly node: ['Computation'];
+ uid: string;
+ uuid: string;
+ citation?: IReference[];
+ condition?: ICondition[];
+ model_version: string;
+ created_at: string;
+ updated_at: string;
+ input_data?: IData[];
+ output_data?: IData[];
+ locked: boolean;
+ public: boolean;
+ name: string;
+ notes: string;
+ prerequisite_computation?: IComputation;
+ software_configuration?: ISoftwareConfiguration[];
+ type: string;
+ experiment?: IExperiment[];
+}

scripts/typescript/src/types/cript/IComputationProcess.ts

@@ -0,0 +1,27 @@
+import { ICondition, IData, IReference, ISoftwareConfiguration, ICitation, IExperiment, IIngredient, IProperty } from '.';
+
+/**
+ * A computational_process is a simulation that processes or changes a virtual material.
+ * @see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=13
+ */
+export interface IComputationProcess {
+ readonly node: ['ComputationProcess'];
+ uid: string;
+ uuid: string;
+ type: string;
+ citation?: ICitation[];
+ condition?: ICondition[];
+ model_version: string;
+ created_at: string;
+ updated_at: string;
+ input_data?: IData[];
+ output_data?: IData[];
+ locked: boolean;
+ public: boolean;
+ name: string;
+ notes: string;
+ software_configuration?: ISoftwareConfiguration[];
+ experiment?: IExperiment[];
+ ingredient?: IIngredient[];
+ property?: IProperty[];
+}

scripts/typescript/src/types/cript/ICondition.d.ts

@@ -0,0 +1,19 @@
+import { IData } from '.';
+
+export interface ICondition {
+ readonly node: ['Condition'];
+ data?: IData[];
+ created_at?: string;
+ updated_at?: string;
+ descriptor?: string;
+ key: string;
+ measurement_id?: number;
+ model_version?: string;
+ set_id?: number;
+ type?: string;
+ uncertainty?: string;
+ uncertainty_type?: string;
+ unit?: string;
+ uuid?: string;
+ value: string;
+}

scripts/typescript/src/types/cript/IData.ts

@@ -0,0 +1,29 @@
+import { IComputation, IExperiment, IFile, IMaterial, IProcess } from '.';
+
+export interface IData {
+ readonly node: ['Data'];
+ name: string;
+ notes?: string;
+ type?: string;
+ uid?: string;
+ uuid?: string;
+ file?: IFile[];
+ file_count?: number;
+ experiment?: IExperiment[];
+ citation?: []; // ICitation or ReferencePost
+ citation_count?: number;
+ computation_process?: []; //IComputationProcess
+ computation_process_count?: number;
+ process?: IProcess[];
+ process_count?: number;
+ computation?: IComputation[];
+ computation_count?: number;
+ created_at?: string;
+ updated_at?: string;
+ locked?: boolean;
+ public?: boolean;
+ material?: IMaterial[];
+ material_count?: number;
+ model_version?: string;
+ sample_preparation?: string;
+}

scripts/typescript/src/types/cript/IEquipment.ts

@@ -0,0 +1,23 @@
+import { ICitation } from "./ICitation"
+import { ICondition } from "./ICondition";
+import { IFile } from "./IFile";
+
+/**
+ * "Equipment are physical instruments, tools, glassware, etc. used in a process (...)"
+ * @see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=21
+ *
+ * Typing is from from API's schema
+ */
+export interface IEquipment {
+ key: string | undefined; // Not returned bu API yet. (@see https://trello.com/c/ZAR47EVX/10-equipment-schema-key-property-is-missing)
+ citation?: ICitation[];
+ condition?: ICondition[];
+ created_at: string;
+ description: string;
+ file?: IFile[];
+ model_version: string;
+ node: ['Equipment'];
+ uid: string;
+ updated_at: string;
+ uuid: string;
+}

scripts/typescript/src/types/cript/IExperiment.ts

@@ -0,0 +1,25 @@
+import { ICollection, IComputation, IComputationProcess, IData, IMaterial, IProcess } from '.';
+
+export interface IExperiment {
+ computation_count?: number;
+ computation?: IComputation[];
+ computation_process_count?: number;
+ computation_process?: IComputationProcess[];
+ created_at?: string;
+ data?: IData[];
+ data_count?: number;
+ locked?: boolean;
+ material?: IMaterial[]; // this field is not implemented on the new API, but was present in the legacy API and is used in this project.
+ material_count?: number; // TODO: remove auestion mark once new API adds the field.
+ model_version?: string; 
+ name?: string;
+ notes?: string;
+ process?: IProcess[];
+ process_count?: number;
+ public?: boolean;
+ uid?: string;
+ updated_at?: string;
+ uuid?: string;
+ collection?: ICollection[];
+ readonly node: ['Experiment'];
+}

scripts/typescript/src/types/cript/IFile.ts

@@ -0,0 +1,8 @@
+export interface IFile {
+ name: string;
+ notes: string;
+ type: string;
+ uid: string;
+ uuid: string;
+ readonly node: ['File'];
+}

scripts/typescript/src/types/cript/IIdentifier.ts

@@ -0,0 +1,11 @@
+
+/**
+ * @deprecated because identifiers are regular properties on IMaterial node.
+ * 
+ * The data model describe it differently: "Identifiers are a sub-object for the material node and are unique labels or descriptive information for a material (...)"
+ * https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=16
+ */
+export interface IIdentifier {
+ key: string;
+ value: string | number | string[] | number[];
+}

scripts/typescript/src/types/cript/IIngredient.ts

@@ -0,0 +1,83 @@
+import { IMaterial, IQuantity } from ".";
+
+/**
+ * "Ingredients are links to material nodes with the associated quantities. (...)"
+ * Data model says @see https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6322994103e27d9176d5b10c/original/main-supporting-information.pdf#page=21
+ * backend reference:
+ * "IngredientPost": {
+ "$id": "IngredientPost",
+ "additionalProperties": false,
+ "properties": {
+ "created_at": {
+ "default": "now()",
+ "format": "date-time",
+ "readOnly": true,
+ "type": "string"
+ },
+ "keyword": {
+ "enum": [
+ "monomer",
+ "polymer",
+ "initiator",
+ "catalyst",
+ "solvent",
+ "cta",
+ "quench",
+ "reagent",
+ "workup",
+ "intermediate",
+ "computation",
+ "filler",
+ "matrix",
+ "inert_carrier_gas"
+ ],
+ "item": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "material": {
+ "$ref": "MaterialPost"
+ },
+ "model_version": {
+ "$ref": "ModelVersion"
+ },
+ "node": {
+ "const": "Ingredient",
+ "type": "string"
+ },
+ "quantity": {
+ "item": {
+ "$ref": "QuantityPost"
+ },
+ "type": "array"
+ },
+ "updated_at": {
+ "default": "now()",
+ "format": "date-time",
+ "readOnly": true,
+ "type": "string"
+ },
+ "uuid": {
+ "default": "uuid()",
+ "readOnly": true,
+ "type": "string"
+ }
+ },
+ "required": [
+ "node",
+ "material"
+ ],
+ "type": "object"
+ } 
+*/
+export interface IIngredient {
+ material?: IMaterial[];
+ quantity?: IQuantity[];
+ created_at?: string;
+ keyword?: string[];
+ model_version?: string;
+ node: ['Ingredient'];
+ updated_at?: string;
+ uuid?: string;
+}

scripts/typescript/src/types/cript/IInventory.ts

@@ -0,0 +1,13 @@
+import { ICollection, IMaterial } from '.';
+
+export interface IInventory {
+ name: string;
+ notes?: string;
+ material_count?: number;
+ material?: IMaterial[];
+ public?: boolean;
+ uid?: string;
+ uuid?: string;
+ collection?: ICollection[];
+ readonly node: ['Inventory'];
+}