feat: Implement warning for sidecar overrides

src/issues/list.ts

@@ -166,6 +166,10 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'A json sidecar file was found without a corresponding data file',
   },
+  SIDECAR_FIELD_OVERRIDE: {
+    severity: 'warning',
+    reason: 'Sidecar files should not override values assigned at a higher level.',
+  },
   BLACKLISTED_MODALITY: {
     severity: 'error',
     reason: 'The modality in this file is blacklisted through validator configuration.',

src/schema/context.test.ts

@@ -1,4 +1,4 @@
-import { assert, assertObjectMatch } from '@std/assert'
+import { assert, assertEquals, assertObjectMatch } from '@std/assert'
 import type { DatasetIssues } from '../issues/datasetIssues.ts'
 import { BIDSContext } from './context.ts'
 import { dataFile, rootFileTree } from './fixtures.test.ts'
@@ -21,6 +21,12 @@ Deno.test('test context LoadSidecar', async (t) => {
       anatValue: 'anat',
     })
   })
+  await t.step('Warnings are emitted for overriding sidecar fields', () => {
+    assertEquals(
+      context.dataset.issues.get({ code: 'SIDECAR_FIELD_OVERRIDE' }).length,
+      2,
+    )
+  })
 })
 
 Deno.test('test context loadSubjects', async (t) => {

src/schema/context.ts

@@ -208,14 +208,26 @@ export class BIDSContext implements Context {
       }
     }
     for (const file of sidecars) {
-      const json = await loadJSON(file).catch((error) => {
+      const json = await loadJSON(file).catch((error): Record<string, unknown> => {
         if (error.key) {
           this.dataset.issues.add({ code: error.key, location: file.path })
           return {}
         } else {
           throw error
         }
       })
+      const overrides = Object.keys(this.sidecar).filter((x) => Object.hasOwn(json, x))
+      for (const key of overrides) {
+        if (json[key] !== this.sidecar[key]) {
+          const overrideLocation = this.sidecarKeyOrigin[key]
+          this.dataset.issues.add({
+            code: 'SIDECAR_FIELD_OVERRIDE',
+            subCode: key,
+            location: overrideLocation,
+            issueMessage: `Sidecar key defined in ${file.path} overrides previous value (${json[key]}) from ${overrideLocation}`,
+          })
+        }
+      }
       this.sidecar = { ...json, ...this.sidecar }
       Object.keys(json).map((x) => this.sidecarKeyOrigin[x] ??= file.path)
     }