Check every index read, everywhere: noUncheckedIndexedAccess in tsconfig.json

.github/workflows/tests.yml

@@ -87,12 +87,6 @@ jobs:
       - name: Lint
         run: npm run check:lint
 
-      # noUncheckedIndexedAccess is a compiler flag with no warning level, so it
-      # is held at a per-file count until it reaches zero and can be enabled
-      # (#345). Like the lint warnings, a count can only go down.
-      - name: Unchecked indexed access has not increased
-        run: npm run check:indexed
-
       # eslint sees unused symbols within a file; knip sees whole files and
       # exports nothing imports, which was the bigger pile. Also baselined,
       # because some findings need someone who knows the data model to judge --

e2e/reacfoam.spec.ts

@@ -58,7 +58,9 @@ async function centreOf(page: Page, label: string) {
 function darkInTitleStrip(page: Page) {
   return page.evaluate(() => {
     const canvases = [...document.querySelectorAll<HTMLCanvasElement>('cr-reacfoam canvas')];
-    const { width, height } = canvases[0];
+    const [first] = canvases;
+    if (!first) throw new Error('no reacfoam canvas');
+    const { width, height } = first;
     const top = Math.floor(height * 0.85);
     const all = document.createElement('canvas');
     all.width = width;

package.json

@@ -40,7 +40,6 @@
     "lint": "eslint .",
     "lint:fix": "eslint . --fix",
     "check:lint": "node scripts/check-lint.mjs",
-    "check:indexed": "node scripts/check-indexed-access.mjs",
     "check:dead": "node scripts/check-dead-code.mjs",
     "check:lockfile": "node scripts/check-lockfile.mjs",
     "dead": "knip",

projects/reactome-diagram-element/tsconfig.app.json

@@ -2,10 +2,7 @@
   "extends": "../../tsconfig.json",
   "compilerOptions": {
     "outDir": "../../out-tsc/reactome-diagram-element",
-    "types": [],
-    // Every index read checked (#345). Not yet in tsconfig.json: the workspace
-    // libraries have findings left, held at a count by scripts/check-indexed-access.mjs.
-    "noUncheckedIndexedAccess": true
+    "types": []
   },
   "files": ["src/main.ts"],
   "include": ["../pathway-browser/src/**/*.d.ts", "../../src/**/*.d.ts"]

projects/reactome-gsa-form/src/lib/dataset-form/datasets/select-dataset/dataset-types/local-data/local-data.component.ts

@@ -141,10 +141,9 @@ export class LocalDataComponent {
         }
         const lines = text.trim().split('\n');
 
-        for (let i = 1; i < lines.length; i++) {
-          const columns = lines[i].split('\t');
-          for (let j = 1; j < columns.length; j++) {
-            const value = columns[j].trim();
+        for (const line of lines.slice(1)) {
+          for (const column of line.split('\t').slice(1)) {
+            const value = column.trim();
             if (!Number.isInteger(Number(value))) {
               return resolve(false);
             }
@@ -166,10 +165,10 @@ export class LocalDataComponent {
         this.readFile(fileRibo),
       ]);
 
-      const file1FirstLine = file1Content.split('\n')[0].trim();
-      const file2FirstLine = file2Content.split('\n')[0].trim();
+      const [file1FirstLine = ''] = file1Content.split('\n');
+      const [file2FirstLine = ''] = file2Content.split('\n');
 
-      return file1FirstLine === file2FirstLine;
+      return file1FirstLine.trim() === file2FirstLine.trim();
     } catch (error) {
       return false;
     }

projects/reactome-gsa-form/src/lib/dataset-form/datasets/statistical-design/statistical-design.component.ts

@@ -74,7 +74,7 @@ export class StatisticalDesignComponent implements OnInit {
     this.store.dispatch(datasetActions.setCovariatesValue({ id: this.datasetId(), value: value }));
   }
 
-  comparisonGroup2Values(groups: string[], group1: string) {
+  comparisonGroup2Values(groups: string[] | undefined, group1: string) {
     if (!groups) return [];
     return groups.filter((group) => group !== group1);
   }

projects/reactome-gsa-form/src/lib/services/analysis-methods.service.ts

@@ -6,14 +6,24 @@ import { extractErrorMessage } from '../utilities/utils';
 import { MatSnackBar } from '@angular/material/snack-bar';
 import { ConfigProvider, REACTOME_GSA_CONFIG } from '../config/gsa-config';
 
-export const typeToParse: { [p: string]: (value: string) => any } = {
+/** Reads a parameter's text as its type: a boolean, a number, or the text itself. */
+type Parser = (value: string) => any;
+
+const typeToParse: { [p: string]: Parser } = {
   bool: (value) => value.toLowerCase() === 'true',
   float: parseFloat,
   int: parseInt,
   email: (value) => value,
   string: (value) => value,
 };
 
+/**
+ * How to read a parameter of this type. A type this form does not know -- one
+ * the service added since -- is read as text, rather than taking the whole form
+ * down with it.
+ */
+export const parserFor = (type: string): Parser => typeToParse[type] ?? ((text: string) => text);
+
 @Injectable({
   providedIn: 'root',
 })

projects/reactome-gsa-form/src/lib/services/parse-parameter.spec.ts

@@ -0,0 +1,18 @@
+import { describe, expect, it } from 'vitest';
+import { parserFor } from './analysis-methods.service';
+
+// A method's parameters come from the GSA service, typed by name. A type this
+// form does not know -- one added since -- is read as text rather than taking
+// the form down.
+describe('parserFor', () => {
+  it('reads each known type', () => {
+    expect(parserFor('bool')('True')).toBe(true);
+    expect(parserFor('float')('0.05')).toBe(0.05);
+    expect(parserFor('int')('7')).toBe(7);
+    expect(parserFor('string')('x')).toBe('x');
+  });
+
+  it('reads a type it does not know as text', () => {
+    expect(parserFor('ratio')('1:2')).toBe('1:2');
+  });
+});

projects/reactome-gsa-form/src/lib/state/dataset-source/dataset-source.effect.ts

@@ -3,7 +3,7 @@ import { Injectable, inject } from '@angular/core';
 import { catchError, exhaustMap, map, mergeMap, of, take } from 'rxjs';
 import { FetchDatasetService } from '../../services/fetch-dataset.service';
 import { datasetSourceActions } from './dataset-source.action';
-import { typeToParse } from '../../services/analysis-methods.service';
+import { parserFor } from '../../services/analysis-methods.service';
 
 @Injectable()
 export class DatasetSourceEffects {
@@ -50,8 +50,8 @@ export class DatasetSourceEffects {
             externals.forEach((external) =>
               external.parameters.forEach((param) => {
                 //  param.id = `${external.id} - ${param.name}`;
-                param.value = typeToParse[param.type](param.default);
-                param.default = typeToParse[param.type](param.default);
+                param.value = parserFor(param.type)(param.default);
+                param.default = parserFor(param.type)(param.default);
               })
             );
             return externals;

projects/reactome-gsa-form/src/lib/state/dataset/dataset.effect.ts

@@ -211,7 +211,8 @@ export class DatasetEffects {
               ['', ...summary.sample_metadata.map((col) => col.name)],
               ...summary.sample_ids.map((sampleId, i) => [
                 sampleId,
-                ...summary.sample_metadata!.map((column) => column.values[i]),
+                // A missing value stays missing (sent as null), as it always was.
+                ...summary.sample_metadata!.map((column) => column.values[i] as string),
               ]),
             ];
         return datasetActions.setAnnotations({ annotations: table, id });

projects/reactome-gsa-form/src/lib/state/dataset/dataset.reducer.ts

@@ -134,13 +134,14 @@ export const datasetReducer: ActionReducer<DatasetState> = createReducer(
           const annotations = dataset.annotations!;
 
           const annotationsWithSimpleIds = cp(annotations);
-          annotationsWithSimpleIds[0][0] = 'sample_ids';
+          const [header] = annotationsWithSimpleIds;
+          if (header) header[0] = 'sample_ids';
 
           return {
             id: dataset.id,
             changes: {
               annotationColumns: new Map<string, string[]>(
-                transpose(annotationsWithSimpleIds).map((col) => [col[0], col.slice(1)])
+                transpose(annotationsWithSimpleIds).map((col) => [col[0] ?? '', col.slice(1)])
               ),
             },
           };
@@ -213,7 +214,7 @@ export const datasetReducer: ActionReducer<DatasetState> = createReducer(
         ...dataset.statisticalDesign!,
         covariances:
           dataset.annotations?.[0]
-            .slice(1) //slice the first element, which is the empty string
+            ?.slice(1) //slice the first element, which is the empty string
             .filter((name) => name !== dataset.statisticalDesign!.analysisGroup)
             .map((name) => ({
               name,

projects/reactome-gsa-form/src/lib/state/dataset/dataset.selector.ts

@@ -84,7 +84,7 @@ export const datasetFeature = createFeature({
           .slice(1) // Remove row ids column
           .map((column) => ({
             // Create groups with distinct values
-            name: column[0],
+            name: column[0] ?? '',
             values: new Set(column.slice(1).filter((s) => s)),
           }))
           .filter((group) => group.values.size >= 2) // Filter groups suitable for analysis
@@ -115,19 +115,20 @@ export const datasetFeature = createFeature({
           .slice(1) // Remove row ids column
           .map((column) => ({
             // Create groups with distinct values
-            name: column[0],
+            name: column[0] ?? '',
             values: column.slice(1),
           }))
           .filter((column) => dataset!.statisticalDesign!.analysisGroup !== column.name) // Remove analysis group
           .filter((column) => {
-            const group1Values = new Set<string>();
-            const group2Values = new Set<string>();
+            // A missing value counts as one, as it always has.
+            const group1Values = new Set<string | undefined>();
+            const group2Values = new Set<string | undefined>();
             for (let i = 0; i < analysisColumn.length; i++) {
               const analysedValue = analysisColumn[i];
               for (const [comparisonGroup, values] of [
                 [dataset!.statisticalDesign!.comparisonGroup1, group1Values],
                 [dataset!.statisticalDesign!.comparisonGroup2, group2Values],
-              ] as [string, Set<string>][]) {
+              ] as [string, Set<string | undefined>][]) {
                 if (analysedValue === comparisonGroup) {
                   const value = column.values[i];
                   if (values.has(value)) return false; // remove columns where a "pair" is associated more than once to the same condition

projects/reactome-gsa-form/src/lib/state/method/method.effect.ts

@@ -1,6 +1,6 @@
 import { Actions, createEffect, ofType } from '@ngrx/effects';
 import { Injectable, inject } from '@angular/core';
-import { AnalysisMethodsService, typeToParse } from '../../services/analysis-methods.service';
+import { AnalysisMethodsService, parserFor } from '../../services/analysis-methods.service';
 import { methodActions } from './method.action';
 import { catchError, exhaustMap, map, of } from 'rxjs';
 import { ParameterType } from '../../model/methods.model';
@@ -21,8 +21,8 @@ export class MethodEffects {
             methods.forEach((method) => {
               method.parameters.forEach((param) => {
                 param.type = param.name === 'email' ? ParameterType.email : param.type;
-                param.value = typeToParse[param.type](param.default);
-                param.default = typeToParse[param.type](param.default);
+                param.value = parserFor(param.type)(param.default);
+                param.default = parserFor(param.type)(param.default);
               });
               const server = method.parameters.find((param) => param.name === 'reactome_server');
               if (server) server.value = this.config().server;

projects/reactome-gsa-form/src/lib/state/method/method.reducer.ts

@@ -15,7 +15,8 @@ export const methodReducer: ActionReducer<MethodState> = createReducer(
       })),
       {
         ...state,
-        commonParameters: methods[0].parameters.filter((param) => param.scope === 'common'), // They are transferred to global status
+        // They are transferred to global status; no methods have none.
+        commonParameters: methods[0]?.parameters.filter((param) => param.scope === 'common') ?? [],
       }
     )
   ),

projects/reactome-gsa-form/src/lib/utilities/species/species.pipe.ts

@@ -4,6 +4,7 @@ import { Pipe, PipeTransform } from '@angular/core';
 export class SpeciesPipe implements PipeTransform {
   transform(value: string): unknown {
     const words = value.split(' ');
-    return words[0].charAt(0).toUpperCase() + '. ' + words.slice(1).join(' ');
+    const [genus = ''] = words;
+    return genus.charAt(0).toUpperCase() + '. ' + words.slice(1).join(' ');
   }
 }

projects/reactome-table/src/lib/component/table/table.component.html

@@ -147,7 +147,7 @@
             @if (settings.addRow) {
               <tr>
                 <th class="rows">...</th>
-                <td class="no-padding add-row-button-container" [colSpan]="data[0].length">
+                <td class="no-padding add-row-button-container" [colSpan]="data[0]?.length ?? 1">
                   <button
                     (click)="addRow()"
                     (keydown.shift.tab)="focusLastCell($event)"