feat: add logger components (#709)

Adds `FifoLoggerProvider`, `FifoLoggerDialog`, `FifoLoggerToolbarItem`, `useFifoLogger`, `useFifoLogs` to the API Closes: #449
zakodium-oss · Apr 12, 2024 · 30b6212 · 30b6212
1 parent 69ba0eb
commit 30b6212
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Showing 22 changed files with 355 additions and 114 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -60,6 +60,7 @@
   "peerDependencies": {
     "@blueprintjs/core": "^5.3.2",
     "@blueprintjs/icons": "^5.1.7",
+    "fifo-logger": "^1.0.0",
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
@@ -128,6 +129,7 @@
     "eslint": "^8.57.0",
     "eslint-config-zakodium": "^8.1.0",
     "eslint-plugin-storybook": "^0.8.0",
+    "fifo-logger": "^1.0.0",
     "prettier": "^3.2.5",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",

diff --git a/src/app-data/loaders/biologicLoader.ts b/src/app-data/loaders/biologicLoader.ts
@@ -1,11 +1,11 @@
 import { parseMPR, parseMPT } from 'biologic-converter';
 import type { MeasurementVariable } from 'cheminfo-types';
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 
-import type { Measurements, MeasurementBase } from '../index';
+import type { MeasurementBase, Measurements } from '../index';
 
 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 */
@@ -18,7 +18,7 @@ type MeasurementDataVariable = Record<string, MeasurementVariable>;
  */
 export async function biologicLoader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
   const measurements: Partial<Measurements> = {};
   const entries: MeasurementBase[] = [];
@@ -67,14 +67,15 @@ export async function biologicLoader(
     } catch (error) {
       //send error to UI to show to User ?
       if (error instanceof Error) {
-        if (logs) {
-          logs.push(createLogEntry({ error, relativePath: file.relativePath }));
+        if (logger) {
+          logger.error(error);
         } else {
           throw error;
         }
       }
     }
   }
+  logger?.debug(`Loaded ${entries.length} entries with biologicLoader`);
   measurements.iv = { entries };
   return measurements;
 }

diff --git a/src/app-data/loaders/cdfLoader.ts b/src/app-data/loaders/cdfLoader.ts
@@ -1,18 +1,19 @@
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 import { NetCDFReader } from 'netcdfjs';
 
 import { assert } from '../../components/index';
-import type { MeasurementBase, Measurements, MeasurementKind } from '../index';
+import type { MeasurementBase, MeasurementKind, Measurements } from '../index';
 
 import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-import { ParserLog, createLogEntry } from './utility/parserLog';
 
 export async function cdfLoader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
   const newMeasurements: Partial<Measurements> = {};
   let kind: MeasurementKind | undefined;
+  let count = 0;
   for (const file of fileCollection) {
     if (/\.cdf$/i.test(file.name)) {
       try {
@@ -57,26 +58,20 @@ export async function cdfLoader(
               : chromatogram(reader),
         };
         newMeasurements[kind]?.entries.push(newMeasurement);
+        count++;
       } catch (error) {
         if (error instanceof Error) {
           //send error to UI ?
-          if (logs) {
-            logs.push(
-              createLogEntry({
-                error,
-                parser: 'cdfLoader',
-                message: 'error parsing file from cdfLoader',
-                relativePath: file.relativePath,
-              }),
-            );
+          if (logger) {
+            logger.error(error);
           } else {
             throw error;
           }
         }
       }
     }
   }
-
+  logger?.debug(`Loaded ${count} measurements with cdfLoader`);
   return newMeasurements;
 }
 

diff --git a/src/app-data/loaders/jcampLoader.ts b/src/app-data/loaders/jcampLoader.ts
@@ -1,11 +1,11 @@
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 import { convert } from 'jcampconverter';
 
 import { assert } from '../../components/index';
 import type { MeasurementKind, Measurements } from '../index';
 
 import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-import { createLogEntry, ParserLog } from './utility/parserLog';
 
 /**
  *
@@ -15,8 +15,9 @@ import { createLogEntry, ParserLog } from './utility/parserLog';
  */
 export async function jcampLoader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
+  let count = 0;
   const newMeasurements: Partial<Measurements> = {};
   for (const file of fileCollection) {
     if (/(?:\.jdx|\.dx)$/i.test(file.name)) {
@@ -50,22 +51,15 @@ export async function jcampLoader(
               meta: measurement.meta,
               data: normalizeSpectra(measurement.spectra),
             };
+            count++;
             Object.assign(newMeasurement.info, measurement.info);
             newMeasurements[kind]?.entries.push(newMeasurement);
           }
         }
       } catch (error) {
-        // send error to UI ?
         if (error instanceof Error) {
-          if (logs) {
-            logs.push(
-              createLogEntry({
-                error,
-                parser: 'jcamp converter',
-                relativePath: file.relativePath,
-                message: 'error parsing jdx or dx file',
-              }),
-            );
+          if (logger) {
+            logger?.error(error);
           } else {
             throw error;
           }
@@ -74,6 +68,7 @@ export async function jcampLoader(
     }
   }
 
+  logger?.debug(`Loaded ${count} measurements with jcampLoader`);
   return newMeasurements;
 }
 

diff --git a/src/app-data/loaders/loadMeasurements.ts b/src/app-data/loaders/loadMeasurements.ts
@@ -1,7 +1,8 @@
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 import { xMinMaxValues } from 'ml-spectra-processing';
 
-import { Measurements, enhance, Enhancers, MeasurementBase } from '../index';
+import { enhance, Enhancers, MeasurementBase, Measurements } from '../index';
 
 import {
   MeasurementsLoader,
@@ -12,20 +13,20 @@ import type { ParserLog } from './utility/parserLog';
 export interface LoadOptions {
   loaders?: MeasurementsLoader[];
   enhancers?: Partial<Enhancers>;
-  logger?: boolean;
+  logger?: FifoLogger;
 }
 
 export async function loadMeasurements(
   fileCollection: FileCollection,
-  options: LoadOptions = {},
+  options: LoadOptions,
 ) {
   const measurements: Partial<Measurements> = {};
   const logs: ParserLog[] = [];
-  const { loaders = [], enhancers = {}, logger = true } = options;
+  const { loaders = [], enhancers = {}, logger } = options;
   for (const loader of loaders) {
     // TODO: load in parallel
     // eslint-disable-next-line no-await-in-loop
-    const loaderData = await loader(fileCollection, logger ? logs : undefined);
+    const loaderData = await loader(fileCollection, logger);
     for (const { entries } of Object.values(loaderData)) {
       for (const entry of entries) {
         computeMinMax(entry);

diff --git a/src/app-data/loaders/proprietary/agilent/cary500Loader.ts b/src/app-data/loaders/proprietary/agilent/cary500Loader.ts
@@ -1,16 +1,15 @@
-import type { FileCollectionItem, FileCollection } from 'filelist-utils';
+import type { FifoLogger } from 'fifo-logger';
+import type { FileCollection, FileCollectionItem } from 'filelist-utils';
 
 import {
-  Measurements,
-  MeasurementBase,
   getMeasurementInfoFromFile,
-  ParserLog,
-  createLogEntry,
+  MeasurementBase,
+  Measurements,
 } from '../../../index';
 
 export async function cary500Loader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
   const newMeasurements: Partial<Measurements> = {};
   const entries: MeasurementBase[] = [];
@@ -26,23 +25,16 @@ export async function cary500Loader(
         }
       } catch (error) {
         if (error instanceof Error) {
-          if (logs) {
-            logs.push(
-              createLogEntry({
-                kind: 'error',
-                parser: 'cary500Loader',
-                message: 'Error parsing cary500 experiment.',
-                error,
-                relativePath: file.relativePath,
-              }),
-            );
+          if (logger) {
+            logger.error(error);
           } else {
             throw error;
           }
         }
       }
     }
   }
+  logger?.debug(`Loaded ${entries.length} entries with cary500Loader`);
   newMeasurements.uvvis = { entries };
   return newMeasurements;
 }

diff --git a/src/app-data/loaders/spcLoader.ts b/src/app-data/loaders/spcLoader.ts
@@ -1,11 +1,11 @@
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
-import { parse, guessSpectraType } from 'spc-parser';
+import { guessSpectraType, parse } from 'spc-parser';
 
 import { assert } from '../../components/index';
-import type { MeasurementKind, Measurements, MeasurementBase } from '../index';
+import type { MeasurementBase, MeasurementKind, Measurements } from '../index';
 
 import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-import { ParserLog, createLogEntry } from './utility/parserLog';
 
 /**
  *
@@ -15,7 +15,7 @@ import { ParserLog, createLogEntry } from './utility/parserLog';
  */
 export async function spcLoader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
   const measurements: Partial<Measurements> = {};
   for (const file of fileCollection) {
@@ -38,14 +38,8 @@ export async function spcLoader(
           data: parsed.spectra as unknown as MeasurementBase['data'],
         });
       } catch (error) {
-        if (error instanceof Error && logs) {
-          logs.push(
-            createLogEntry({
-              parser: 'spc-parser',
-              relativePath: file.relativePath,
-              error,
-            }),
-          );
+        if (error instanceof Error && logger) {
+          logger.error(error);
         } else {
           throw error;
         }

diff --git a/src/app-data/loaders/utility/measurementLoader.ts b/src/app-data/loaders/utility/measurementLoader.ts
@@ -1,13 +1,12 @@
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 
 import { assert } from '../../../components/index';
 import type { MeasurementBase, Measurements } from '../../index';
 
-import type { ParserLog } from './parserLog';
-
 export type MeasurementsLoader = (
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ) => Promise<Partial<Measurements>>;
 
 export function mergeMeasurements(

diff --git a/src/app-data/loaders/wdfLoader.ts b/src/app-data/loaders/wdfLoader.ts
@@ -1,11 +1,11 @@
 import { MeasurementVariable } from 'cheminfo-types';
+import type { FifoLogger } from 'fifo-logger';
 import type { FileCollection } from 'filelist-utils';
 import { parse, Wdf } from 'wdf-parser';
 
-import type { Measurements, MeasurementBase } from '../index';
+import type { MeasurementBase, Measurements } from '../index';
 
 import { getMeasurementInfoFromFile } from './utility/getMeasurementInfoFromFile';
-import { ParserLog, createLogEntry } from './utility/parserLog';
 
 /**
  *
@@ -15,7 +15,7 @@ import { ParserLog, createLogEntry } from './utility/parserLog';
  */
 export async function wdfLoader(
   fileCollection: FileCollection,
-  logs?: ParserLog[],
+  logger?: FifoLogger,
 ): Promise<Partial<Measurements>> {
   const measurements: Partial<Measurements> = {};
   const entries: MeasurementBase[] = [];
@@ -33,15 +33,8 @@ export async function wdfLoader(
         });
       } catch (error) {
         if (error instanceof Error) {
-          if (logs) {
-            logs.push(
-              createLogEntry({
-                parser: 'wdf',
-                error,
-                message: 'error reading wdf file',
-                relativePath: file.relativePath,
-              }),
-            );
+          if (logger) {
+            logger.error(error);
           } else {
             throw error;
           }