refactor: update loaders to support error logs (#354)

package.json

@@ -67,7 +67,7 @@
     "@lukeed/uuid": "^2.0.0",
     "@popperjs/core": "^2.11.6",
     "@tanstack/react-table": "^8.5.22",
-    "biologic-converter": "^0.4.0",
+    "biologic-converter": "^0.5.0",
     "cheminfo-types": "^1.4.0",
     "d3-scale-chromatic": "^3.0.0",
     "filelist-utils": "^1.2.0",

src/app-data/DataState.ts

@@ -4,6 +4,7 @@ import { assert } from '../utils/assert';
 
 import type { IRMeasurement } from './IRMeasurement';
 import type { MeasurementBase } from './MeasurementBase';
+import type { ParserLog } from './loaders/utility/parserLog';
 
 export interface DataState {
   measurements: Measurements;
@@ -63,6 +64,7 @@ export const kindsLabel: Record<MeasurementKind, string> = {
 
 export type Loader = (
   fileCollection: FileCollection,
+  logs?: ParserLog[],
 ) => Promise<Partial<Measurements>>;
 
 export function mergeMeasurements(

src/app-data/__tests__/getGCMSMeasurement.test.ts

@@ -11,7 +11,7 @@ const filteredFileCollection = fileCollection.filter(
 );
 
 test('getGCMSMeasurement', async () => {
-  const measurements = await loadMeasurements(filteredFileCollection, {
+  const { measurements } = await loadMeasurements(filteredFileCollection, {
     loaders: [cdfLoader],
   });
   const result = measurements.gclcms?.entries;

src/app-data/__tests__/getHPLCMeasurement.test.ts

@@ -11,7 +11,7 @@ const filteredFileCollection = fileCollection.filter(
 );
 
 test('getHPLCMeasurement', async () => {
-  const measurements = await loadMeasurements(filteredFileCollection, {
+  const { measurements } = await loadMeasurements(filteredFileCollection, {
     loaders: [cdfLoader],
   });
   const result = measurements.gclc?.entries || [];

src/app-data/__tests__/getIRMeasurement.ts

@@ -19,7 +19,7 @@ export async function getIRMeasurement() {
     (file) => file.name === 'ir.jdx',
   );
 
-  const measurements = await loadMeasurements(filteredFileCollection, {
+  const { measurements } = await loadMeasurements(filteredFileCollection, {
     loaders,
     enhancers,
   });

src/app-data/__tests__/getIVMeasurement.test.ts

@@ -13,6 +13,6 @@ const loaders = [biologicLoader];
 
 async function getIVMeasurement() {
   const fileCollection = await getTestFileCollection('biologic');
-  const measurements = await loadMeasurements(fileCollection, { loaders });
+  const { measurements } = await loadMeasurements(fileCollection, { loaders });
   return measurements.iv || { entries: [] };
 }

src/app-data/__tests__/loadMeasurements.test.ts

@@ -18,13 +18,13 @@ const enhancers = {
 test('loadMeasurements function', async () => {
   const fileCollection = await getTestFileCollection();
 
-  const measurements = await loadMeasurements(fileCollection, {
+  const { measurements } = await loadMeasurements(fileCollection, {
     loaders,
     enhancers,
   });
 
-  expect(Object.keys(measurements)).toStrictEqual(['nmr', 'ir', 'uv', 'raman']);
   const { ir, raman, uv } = measurements;
+  expect(Object.keys(measurements)).toStrictEqual(['nmr', 'ir', 'uv', 'raman']);
   expect(ir?.entries).toHaveLength(2);
 
   expect(ir?.entries[0].peaks).toHaveLength(18);

src/app-data/loadMeasurements.ts

@@ -1,23 +1,26 @@
 import type { FileCollection } from 'filelist-utils';
 
-import { Loader, Measurements, mergeMeasurements } from './DataState';
+import { Measurements, Loader, mergeMeasurements } from './DataState';
 import { enhance } from './enhancers/enhance';
+import type { ParserLog } from './loaders/utility/parserLog';
 
 interface LoadOptions {
   loaders?: Loader[];
   enhancers?;
+  logger?: boolean;
 }
 
 export async function loadMeasurements(
   fileCollection: FileCollection,
   options: LoadOptions = {},
 ) {
   const measurements: Partial<Measurements> = {};
-  const { loaders = [], enhancers = {} } = options;
+  let logs: ParserLog[] = [];
+  const { loaders = [], enhancers = {}, logger = true } = options;
   for (const loader of loaders) {
-    const loaderData = await loader(fileCollection);
+    const loaderData = await loader(fileCollection, logger ? logs : undefined);
     enhance(loaderData, enhancers);
     mergeMeasurements(measurements, loaderData);
   }
-  return measurements;
+  return { measurements, logs };
 }

src/app-data/loaders/biologicLoader.ts

@@ -1,55 +1,72 @@
-import { v4 } from '@lukeed/uuid';
-import { convert } from 'biologic-converter';
+import { parseMPR, parseMPT } from 'biologic-converter';
 import type { MeasurementVariable } from 'cheminfo-types';
 import type { FileCollection } from 'filelist-utils';
 
 import type { Measurements } from '../DataState';
 import type { MeasurementBase } from '../MeasurementBase';
 
+import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
+import { createLogEntry, ParserLog } from './utility/parserLog';
+
 /* the MeasurementBase has got a data key,
  and inside a variable key, compatible with this type */
 type MeasurementDataVariable = Record<string, MeasurementVariable>;
 /**
- * Loader for biologic files, using biologic-converter
- * @param fileCollection
- * @returns iv-MeasurementBase for each file in the collection
+ *
+ * @param fileCollection - the dragged file/files
+ * @param logs - pass to append errors to the logs, it mutates the external array.
+ * @returns - new measurements object to be merged
  */
-export async function biologicLoader(fileCollection: FileCollection) {
+export async function biologicLoader(
+  fileCollection: FileCollection,
+  logs?: ParserLog[],
+): Promise<Partial<Measurements>> {
   const measurements: Partial<Measurements> = {};
   const entries: MeasurementBase[] = [];
-  const results = await convert(fileCollection);
-  for (let { dir, mpr, mpt } of results) {
-    const prepare: Partial<MeasurementBase> = {
-      id: v4(),
-      filename: '',
-      path: dir,
-      info: {},
-      title: '',
-    };
-    if (mpr !== undefined) {
-      prepare.meta = { ...mpr.settings.variables };
-      // puts the "useful" variables at x and y for default plot.
-      const variables = preferredXY(prepare.meta.technique, mpr.data.variables);
-      prepare.data = [{ variables }];
-    } else if (mpt !== undefined) {
-      prepare.meta = { ...mpt.settings?.variables };
-      if (mpt.data?.variables) {
+
+  for (const file of fileCollection.files) {
+    try {
+      if (/\.mpr$/i.test(file.name)) {
+        const mpr = parseMPR(await file.arrayBuffer());
+        const info = getMeasurementInfoFromFile(file);
+        const meta = mpr.settings.variables;
         // puts the "useful" variables at x and y for default plot.
-        const variables = preferredXY(
-          prepare.meta?.technique,
-          mpt.data.variables,
-        );
-        prepare.data = [{ variables }];
+        const variables = preferredXY(meta.technique, mpr.data.variables);
+        const result: MeasurementBase = {
+          title: `Experiment: ${meta.technique}`,
+          ...info,
+          meta,
+          data: [{ variables }],
+        };
+        entries.push(result);
+      } else if (/\.mpt$/i.test(file.name)) {
+        const { data, settings } = parseMPT(await file.arrayBuffer());
+        const info = getMeasurementInfoFromFile(file);
+        if (data?.variables) {
+          // puts the "useful" variables at x and y for default plot.
+          const metaData = settings?.variables;
+          const variables = preferredXY(metaData?.technique, data.variables);
+          const result: MeasurementBase = {
+            title: metaData.technique
+              ? `Experiment: ${metaData.technique}`
+              : file.name,
+            ...info,
+            meta: metaData || {},
+            data: [{ variables }],
+          };
+          entries.push(result);
+        }
+      }
+    } catch (error) {
+      //send error to UI to show to User ?
+      if (error instanceof Error) {
+        if (logs) {
+          logs.push(createLogEntry({ error, relativePath: file.relativePath }));
+        } else {
+          throw error;
+        }
       }
     }
-    if (!prepare.data) {
-      // no data ? skip this file
-      // need a way to dispatch an error with the filename and a custom
-      // message
-      continue;
-    }
-    //will notify if the key is not a valid kind
-    entries.push(prepare as MeasurementBase);
   }
   measurements.iv = { entries };
   return measurements;
@@ -73,17 +90,15 @@ function preferredXY(
 
   switch (technique) {
     case 'CA': {
-      //Chronoamperometry or Chronocoulometry
-      variables = setDefault(variables, 'time', 'x');
-      // I am not sure how to find out whether it is Chronoamperometry or Chronocoulometry
-      // (same experiment just changes what user is interested in.)
+      //Chronoamperometry or Chronocoulometry (how distinguish?)
       variables = setDefault(variables, 'I', 'y');
+      variables = setDefault(variables, 'time', 'x');
       break;
     }
     case 'CP': {
       //Chronopotentiometry
+      variables = setDefault(variables, '<Ewe>', 'y');
       variables = setDefault(variables, 'time', 'x');
-      variables = setDefault(variables, '<I>', 'y');
       break;
     }
     case 'CV': {
@@ -92,8 +107,13 @@ function preferredXY(
       variables = setDefault(variables, 'Ewe', 'x');
       break;
     }
+    case 'GCPL': {
+      variables = setDefault(variables, 'Ewe', 'y');
+      variables = setDefault(variables, 'time', 'x');
+      break;
+    }
     default:
-      return variables;
+      break;
   }
   return variables;
 }
@@ -110,8 +130,8 @@ function setDefault(
   label: string,
   storeAt: 'x' | 'y',
 ) {
-  for (let varum in variables) {
-    // find the key that has the label (or skip if not found)
+  for (const varum in variables) {
+    // find the key with `label` (or skip if not found)
     if (
       variables[varum].label === label && //if not already at the right key
       varum !== storeAt
@@ -122,7 +142,7 @@ function setDefault(
         // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
         delete variables[varum];
       } else {
-        // if the storeAt is already occupied, we swap the two
+        // if the storeAt is already occupied, swap the two
         const originalX = variables[storeAt];
         const newX = variables[varum];
         variables[storeAt] = newX;