Merge remote-tracking branch 'origin/master' into fix/deno_2_test_and…

…_build

.github/dependabot.yml

@@ -15,12 +15,3 @@ updates:
     directory: '/'
     schedule:
       interval: 'monthly'
-#   - package-ecosystem: 'npm'
-#     directory: '/'
-#     schedule:
-#       interval: 'weekly'
-#
-#   - package-ecosystem: 'npm'
-#     directory: '/bids-validator-web'
-#     schedule:
-#       interval: 'weekly'

.github/workflows/schema_web_deploy.yml

@@ -14,23 +14,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      # Use Node 18 for legacy build
-      - uses: actions/setup-node@v4
-        with:
-          node-version: 18
-      - uses: denoland/setup-deno@v2
+      - uses: denoland/setup-deno@v1
         with:
           deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - name: Install NPM deps
         run: npm install
-        working-directory: ./legacy
-      - name: Build legacy validator website
-        run: npm run web-export
-        working-directory: ./legacy
-      - name: Move legacy validator build into deno website
-        run: mv legacy/bids-validator-web/out web/dist/legacy
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3
         with:

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "bids-examples"]
-	path = legacy/bids-validator/tests/data/bids-examples
-	url = https://github.com/bids-standard/bids-examples.git

bids-validator/deno.json

@@ -6,7 +6,8 @@
     "./main": "./src/main.ts",
     "./output": "./src/utils/output.ts",
     "./files": "./src/files/deno.ts",
-    "./options": "./src/setup/options.ts"
+    "./options": "./src/setup/options.ts",
+    "./issues": "./src/issues/datasetIssues.ts"
   },
   "publish": {
     "exclude": [
@@ -34,7 +35,7 @@
     "@hed/validator": "npm:[email protected]",
     "@ignore": "npm:[email protected]",
     "@libs/xml": "jsr:@libs/[email protected]",
-    "@mango/nifti": "npm:[email protected].8",
+    "@mango/nifti": "npm:@bids/[email protected].9",
     "@std/assert": "jsr:@std/[email protected]",
     "@std/fmt": "jsr:@std/[email protected]",
     "@std/fs": "jsr:@std/[email protected]",

bids-validator/src/files/deno.ts

@@ -7,6 +7,7 @@ import { type BIDSFile, FileTree } from '../types/filetree.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
 import { FileIgnoreRules, readBidsIgnore } from './ignore.ts'
 import { logger } from '../utils/logger.ts'
+export { type BIDSFile, FileTree }
 
 /**
  * Thrown when a text file is decoded as UTF-8 but contains UTF-16 characters

bids-validator/src/files/nifti.ts

@@ -27,22 +27,11 @@ async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array>
   return result
 }
 
-function readHeaderQuiet(buf: ArrayBuffer) {
-  const console_error = console.error
-  const console_log = console.log
-  console.error = (msg: string) => { logger.info(msg)}
-  console.log = (msg: string) => { logger.info(msg)}
-  const header = readHeader(buf)
-  console.error = console_error
-  console.log = console_log
-  return header
-}
-
 export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
   try {
     const buf = await file.readBytes(1024)
     const data = isCompressed(buf.buffer) ? await extract(buf, 540) : buf
-    const header = readHeaderQuiet(data.buffer)
+    const header = readHeader(data.buffer)
     if (!header) {
       throw { key: 'NIFTI_HEADER_UNREADABLE' }
     }

bids-validator/src/issues/datasetIssues.ts

@@ -1,5 +1,6 @@
 import { nonSchemaIssues } from './list.ts'
-import type { Issue, Severity } from '../types/issues.ts'
+import type { Issue, Severity, IssueDefinition, IssueFile } from '../types/issues.ts'
+export type { Issue, Severity, IssueDefinition, IssueFile }
 
 // Code is deprecated, return something unusual but JSON serializable
 const CODE_DEPRECATED = Number.MIN_SAFE_INTEGER