Merge pull request #12 from C-Accel-CRIPT/feat/rcbc

feat(typescript): add rcbc

scripts/typescript/package.json

@@ -1,21 +1,26 @@
 {
  "name": "cript-typescript",
  "version": "1.0.0",
- "description": "Set of typescript code to convert raw data (*.csv, *.ts) to CRIPT *.json format",
+ "description": "Set of typescript code to convert raw data (*.xlsx, *.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"
+ "build": "npx tsc",
+ "afrl": "npx ts-node ./src/afrl",
+ "bcdb": "npx ts-node ./src/bcdb",
+ "rcbc": "npx ts-node ./src/rcbc",
+ "test": "bash ./test.sh"
  },
  "author": "Bérenger Dalle-Cort, CRIPT, MIT",
  "license": "MIT",
  "dependencies": {
  "csvtojson": "^2.0.10",
+ "jsonstream-ts": "^1.3.6",
  "ts-node": "^10.9.1",
- "typescript": "^5.0.3"
+ "tsconfig-paths": "^4.2.0",
+ "typescript": "^5.0.3",
+ "xlsx": "^0.18.5"
  },
  "devDependencies": {
- "tsconfig-paths": "^4.2.0"
+ "@types/node": "^18.15.12"
  }
 }

scripts/typescript/src/afrl/afrl-csv-to-json.ts

@@ -1,7 +1,7 @@
 import { AFRLData } from "./types"
 import { ICitation, ICollection, ICondition, IInventory, IMaterial, IProject, IProperty, IReference } from "../types/cript"
 import csvtojson from "csvtojson";
-
+import * as fs from 'stream';
 /**
  * This script is a typescript port of @see https://github.com/C-Accel-CRIPT/criptscripts/tree/master/scripts/python_sdk_scripts/AFRL
  * The main difference is the source data is now read from the original CSV and not a preprocessed *.js.
@@ -12,6 +12,9 @@ export type Config = {
  project_name: string;
  // Destination inventory's basename
  inventory_basename: string;
+ // to redirect errors to a stream
+ // By default it will be process.stderr
+ error_stream?: fs.Writable;
 }
 
 export class AFRLtoJSON {
@@ -34,9 +37,12 @@ export class AFRLtoJSON {
  private inventory_polymers: IInventory;
  private inventory_mixtures: IInventory;
 
- private errors: Array<string> = [];
+ private error_stream: fs.Writable;
+
+ constructor(config: Config) {
 
- constructor(config: Config = AFRLtoJSON.load_config()) {
+ this.error_stream = config.error_stream ?? process.stderr;
+ this.error_stream.on('error', e => console.error(e));
 
  // Create inventories
 
@@ -83,10 +89,6 @@ export class AFRLtoJSON {
 
  }
 
- get_errors(): any {
- return [...this.errors];
- }
-
  private get_citation(row: AFRLData): ICitation | undefined {
 
  if(row.reference === undefined) {
@@ -388,11 +390,8 @@ export class AFRLtoJSON {
  return `{{[]${bigsmiles}[]}}`;
  }
 
-
  private record_error(message: string): void {
-
- this.errors.push(message)
- console.error(message);
+ this.error_stream.write(`${message}\n`)
  }
 
  /**
@@ -577,6 +576,7 @@ export class AFRLtoJSON {
  return safe_object;
  });
  console.log(`Assigning default value for string properties OK`);
+
  return afrl_data;
  }
 
@@ -603,7 +603,7 @@ export class AFRLtoJSON {
  // Log failures
  if (failed_rows.length != 0) {
  console.log(`Loading failed. Some objects couldn't be loaded (${failed_rows.length} row(s) failed)`)
- failed_rows.forEach(v => console.error(JSON.stringify(v)))
+ failed_rows.forEach(v => this.record_error(JSON.stringify(v)))
  throw new Error(`${failed_rows.length} row(s) were not loaded.`)
  }
 

scripts/typescript/src/afrl/index.md

@@ -7,10 +7,8 @@ grand_parent: CRIPT Scripts
 
 # AFRL CSV to JSON script
 
-> *Note: this script is a work in progress*
+*note: this script is WIP*
 
-This script converts the Air Force Research Laboratory's CSV file into a unique JSON file. 
-The file can be uploaded at once as a single project into CRIPT.
+This script converts the AFRL CSV file into a unique JSON file. The file can be uploaded at once as a single project into CRIPT.
 
-## TypeScript Script
-* [TypeScript source code](https://github.com/C-Accel-CRIPT/criptscripts/tree/master/scripts/typescript/src/afrl)
+See source code: [Link to TypeScript source code](https://github.com/C-Accel-CRIPT/criptscripts/tree/master/scripts/typescript/src/afrl)

scripts/typescript/src/afrl/index.ts

@@ -6,18 +6,25 @@ import { output_dir_path, write_json_helper } from "@utilities";
 const file_name = 'AFRL_linear_polymer_3pdb_data_csv_4_5_2023.csv'; // TODO: read this from command line argument
 
 // Call main as a promise because low level await are not allowed.
-main().then( code => process.exit(code) )
+main().then( () => process.exit() )
 
-async function main(): Promise<number> {
+async function main() {
 
  console.log('=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=')
  console.log('=-=-=-=-=-=-=-=-=-=-=-=-= AFRL CSV to JSON -=-=-=-=-=-==-=-=-=-=-=-=-=')
  console.log('=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=')
 
+ // Pipe the errors in a file
+ const error_file_path = path.resolve(output_dir_path, 'afrl.errors.txt');
+ const error_file = fs.createWriteStream(error_file_path, { flags: 'w'});
+ error_file.write("Beginnin of the conversion...\n");
+ error_file.write("Second line")
+
  // Instantiate AFRL to JSON serializer
  const serializer = new AFRLCSVtoJSON({
- inventory_basename: 'afrl-deleteme',
- project_name: 'afrl-deleteme'
+ inventory_basename: 'AFRL (dev)',
+ project_name: 'AFRL (dev)',
+ error_stream: error_file
  });
 
  // Load the CSV into an AFRLData[]
@@ -38,11 +45,7 @@ async function main(): Promise<number> {
  console.log('Output folder is ready')
 
  // Write JSON files
-
- write_json_helper(project, 'afrl-transformed', 'minified')
- write_json_helper(project, 'afrl-transformed', 'human-readable')
- write_json_helper(serializer.get_errors(), 'afrl-transformed.errors', 'human-readable')
-
- return 0;
+ await write_json_helper(project, 'afrl', 'minified');
+ await write_json_helper(project, 'afrl', 'human-readable');
 }
 

scripts/typescript/src/rcbc/README.md

@@ -0,0 +1,4 @@
+# RCBC
+
+This script export to CRIPT JSON a statically 
+The JSON is produced by strigifying the main object (project) following a set of rules (cf ../utilities/cript-json.ts)

scripts/typescript/src/rcbc/data/graph/collection.ts

@@ -0,0 +1,11 @@
+import { ICollection } from "@cript";
+import { default_notes } from "./shared";
+import * as experiments from "./experiments";
+
+export const collection: ICollection = {
+ name: "Olsen et al. PPV-b-PI",
+ notes: default_notes,
+ inventory: [],
+ experiment: [...Object.values(experiments)],
+ node: ['Collection']
+};

scripts/typescript/src/rcbc/data/graph/computations.ts

@@ -0,0 +1,38 @@
+import { IComputation } from "@cript";
+import * as datasets from "./datasets";
+
+export const analysis_PPVbPI_42 = {
+ name: '1/T Analysis PPV-b-PI-42',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_42]
+} as IComputation;
+
+export const peak_phase_id_PPVbPI_42 = {
+ name: 'Peak Phase ID PPV-b-PI-42',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_42]
+} as IComputation;
+
+export const analysis_PPVbPI_59 = {
+ name: '1/T Analysis PPV-b-PI-59',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_59]
+} as IComputation;
+
+export const peak_phase_id_PPVbPI_59 = {
+ name: 'Peak Phase ID PPV-b-PI-59',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_59]
+} as IComputation;
+
+export const analysis_PPVbPI_72 = {
+ name: '1/T Analysis PPV-b-PI-72',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_72]
+} as IComputation;
+
+export const peak_phase_id_PPVbPI_72 = {
+ name: 'Peak Phase ID PPV-b-PI-72',
+ node: ['Computation'],
+ input_data: [ datasets.saxs_ppvbpi_72]
+} as IComputation;

scripts/typescript/src/rcbc/data/graph/datasets.ts

@@ -0,0 +1,81 @@
+import { IData } from "@cript";
+
+export const nmr_diether: IData = {
+ name: "NMR diether",
+ node: ["Data"],
+};
+
+export const nmr_aldehyde: IData = {
+ name: "NMR aldehyde",
+ node: ["Data"],
+};
+
+export const gpc_ppv: IData = {
+ name: "GPC PPV",
+ node: ["Data"],
+};
+
+export const density_column_ppv: IData = {
+ name: "Density Column PPV",
+ node: ["Data"],
+};
+
+export const dsc_ppv: IData = {
+ name: "DSC PPV",
+ node: ["Data"],
+};
+
+export const nmr_ppv: IData = {
+ name: "NMR PPV",
+ node: ["Data"],
+};
+
+export const nmr_imine: IData = {
+ name: "NMR imine",
+ node: ["Data"],
+};
+
+export const pom_ppv: IData = {
+ name: "POM PPV",
+ node: ["Data"],
+};
+
+export const gpc_pi_synth_42: IData = {
+ name: "GPC PI-42",
+ node: ["Data"]
+}
+
+export const gpc_pi_synth_59: IData = {
+ name: "GPC PI-59",
+ node: ["Data"]
+}
+
+export const gpc_pi_synth_72: IData = {
+ name: "GPC PI-72",
+ node: ["Data"]
+}
+
+export const gpc_pi_synth_89: IData = {
+ name: "GPC PI-89",
+ node: ["Data"]
+}
+
+export const saxs_ppvbpi_42: IData = {
+ name: "SAXS PPV-b-PI-42",
+ node: ["Data"]
+}
+
+export const saxs_ppvbpi_59: IData = {
+ name: "SAXS PPV-b-PI-59",
+ node: ["Data"]
+}
+
+export const saxs_ppvbpi_72: IData = {
+ name: "SAXS PPV-b-PI-72",
+ node: ["Data"]
+}
+
+export const saxs_ppvbpi_89: IData = {
+ name: "SAXS PPV-b-PI-89",
+ node: ["Data"]
+}