cary500 (#247)

* wip: prepare cary500Loader

* update!: support for fileCollection and guess the spectra type (#246)

* update: support for fileCollection and classification of spectra

* update: a few missing types, and prettify

* test: disable temporarely getIVMeasurement

* chore: rename files to fileCollection

* chore: add todo to use FiltCollection.filter

Co-authored-by: Luc Patiny <luc@patiny.com>

* feat: add experimental cary500Loader

* chore: update dependencies and add testcase

* chore: add missing vitest import

* chore: fix prettier

Co-authored-by: Santiago Miranda <santimir@protonmail.com>

package.json

@@ -51,7 +51,7 @@
     "@tanstack/react-table": "^8.5.15",
     "biologic-converter": "^0.2.0",
     "cheminfo-types": "^1.4.0",
-    "filelist-utils": "^0.12.0",
+    "filelist-utils": "^1.0.1",
     "immer": "^9.0.15",
     "jcampconverter": "^9.0.2",
     "lodash": "^4.17.21",
@@ -76,7 +76,7 @@
     "@types/react-dom": "^18.0.6",
     "@types/react-inspector": "^4.0.2",
     "@vitejs/plugin-react": "^2.1.0",
-    "@vitest/coverage-c8": "^0.24.1",
+    "@vitest/coverage-c8": "^0.24.3",
     "@zakodium/eslint-config": "^6.0.0",
     "babel-loader": "^8.2.5",
     "cheminfo-font": "^1.9.0",
@@ -87,15 +87,15 @@
     "prettier": "^2.7.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "react-icons": "^4.4.0",
+    "react-icons": "^4.6.0",
     "react-inspector": "^6.0.1",
     "react-ocl": "^5.0.0",
     "react-plot": "^0.20.2",
     "rimraf": "^3.0.2",
     "typescript": "^4.8.4",
     "vite": "^3.1.8",
     "vite-tsconfig-paths": "^3.5.1",
-    "vitest": "^0.24.1"
+    "vitest": "^0.24.3"
   },
   "repository": {
     "type": "git",

src/app/context/load.ts

@@ -5,13 +5,14 @@ import { getIRAutoPeakPickingEnhancer } from '../data/enhancers/irAutoPeakPickin
 import { irMeasurementEnhancer } from '../data/enhancers/irMeasurementEnhancer';
 import { biologicLoader } from '../data/loaders/biologicLoader';
 import { jcampLoader } from '../data/loaders/jcampLoader';
+import { cary500Loader } from '../data/loaders/proprietary/agilent/cary500Loader';
 import { spcLoader } from '../data/loaders/spcLoader';
 import { wdfLoader } from '../data/loaders/wdfLoader';
 
 import type { AppDispatch } from './appState';
 
 const options = {
-  loaders: [jcampLoader, spcLoader, wdfLoader, biologicLoader],
+  loaders: [jcampLoader, spcLoader, wdfLoader, biologicLoader, cary500Loader],
   enhancers: {
     ir: [
       irMeasurementEnhancer,

src/app/data/DataState.ts

@@ -20,6 +20,9 @@ export interface Measurements {
   uv: {
     entries: MeasurementBase[];
   };
+  uvvis: {
+    entries: MeasurementBase[];
+  };
   nmr1h: {
     entries: MeasurementBase[];
   };
@@ -42,6 +45,7 @@ export const kindsLabel: Record<MeasurementKind, string> = {
   iv: 'IV',
   raman: 'Raman',
   uv: 'UV',
+  uvvis: 'UV-VIS',
   mass: 'Mass',
   nmr1h: 'NMR 1H',
   other: 'Other',
@@ -64,6 +68,7 @@ export function getEmptyMeasurements(): Measurements {
     iv: { entries: [] },
     raman: { entries: [] },
     uv: { entries: [] },
+    uvvis: { entries: [] },
     nmr1h: { entries: [] },
     mass: { entries: [] },
     other: { entries: [] },

src/app/data/__tests__/append.test.ts

@@ -34,6 +34,7 @@ test('append', async () => {
     'iv',
     'raman',
     'uv',
+    'uvvis',
     'nmr1h',
     'mass',
     'other',

src/app/data/__tests__/getIRMeasurement.ts

@@ -1,6 +1,6 @@
 import { join } from 'path';
 
-import { FileCollection, fileCollectionFromPath } from 'filelist-utils';
+import { fileCollectionFromPath } from 'filelist-utils';
 
 import { getEmptyDataState } from '../DataState';
 import { append } from '../append';
@@ -18,17 +18,11 @@ const enhancers = {
 
 export async function getIRMeasurement() {
   const dataState = getEmptyDataState();
-  const fileCollection = await fileCollectionFromPath(
-    join(__dirname, 'data/jdx/'),
-  );
-  //todo use 'filter' from fileCollection
-  let filteredFileCollection;
-  for (let f of fileCollection) {
-    if (f.name === 'ir.jdx') {
-      filteredFileCollection = new FileCollection([f]);
-      break;
-    }
-  }
+
+  const filteredFileCollection = (
+    await fileCollectionFromPath(join(__dirname, 'data/jdx/'))
+  ).filter((file) => file.name === 'ir.jdx');
+
   const irEntry = (
     await append(filteredFileCollection, dataState, { loaders, enhancers })
   ).dataState.measurements.ir.entries[0];

src/app/data/loaders/proprietary/agilent/__tests__/cary500Loader.test.ts

@@ -0,0 +1,14 @@
+import { join } from 'path';
+
+import { fileCollectionFromPath } from 'filelist-utils';
+import { expect, test } from 'vitest';
+
+import { cary500Loader } from '../cary500Loader';
+
+test('cary500Loader', async () => {
+  const fileCollection = await fileCollectionFromPath(join(__dirname, 'data'));
+  // we should filter to keep only the right data
+  const results = await cary500Loader(fileCollection);
+
+  expect(results.uvvis.entries).toHaveLength(8);
+});