Fixes to allow Deno check to pass and build to succeed.

.github/workflows/deno_tests.yml

@@ -22,10 +22,10 @@ jobs:
       - name: Save describe stamp
         id: describe
         run: echo version=$( git describe ) >> $GITHUB_OUTPUT
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
-      - run: ./build.ts
+          deno-version: v2.x
+      - run: deno --node-modules-dir=auto --allow-env --allow-read --allow-run --allow-net ./build.ts
         working-directory: ./bids-validator
       - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version
       - uses: actions/upload-artifact@v4
@@ -52,14 +52,14 @@ jobs:
           submodules: true
       - uses: denoland/setup-deno@v1
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - name: Set permissions with network access
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --allow-net' >> $GITHUB_ENV
         if: ${{ matrix.allow-net }}
       - name: Set permissions without network access
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --deny-net' >> $GITHUB_ENV
         if: ${{ ! matrix.allow-net }}
-      - run: deno test $PERMS --coverage=cov/ src/
+      - run: deno test --node-modules-dir=auto $PERMS --coverage=cov/ src/
       - name: Collect coverage
         run: deno coverage cov/ --lcov --output=coverage.lcov
         if: ${{ always() }}

.github/workflows/schema_web_build.yml

@@ -17,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - uses: actions/upload-artifact@v4

.github/workflows/schema_web_deploy.yml

@@ -18,9 +18,9 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: 18
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - name: Install NPM deps

bids-validator/deno.json

@@ -31,7 +31,7 @@
     "@bids/schema": "jsr:@bids/[email protected]+d9c23eb0",
     "@cliffy/command": "jsr:@cliffy/[email protected]",
     "@cliffy/table": "jsr:@cliffy/[email protected]",
-    "@hed/validator": "npm:[email protected].4",
+    "@hed/validator": "npm:[email protected].5",
     "@ignore": "npm:[email protected]",
     "@libs/xml": "jsr:@libs/[email protected]",
     "@mango/nifti": "npm:[email protected]",

bids-validator/src/files/browser.test.ts

@@ -4,7 +4,7 @@ import { assertEquals, assertObjectMatch } from '@std/assert'
 import { BIDSFileBrowser, fileListToTree } from './browser.ts'
 
 class TestFile extends File {
-  webkitRelativePath: string
+  override webkitRelativePath: string
   constructor(
     fileBits: BlobPart[],
     fileName: string,

bids-validator/src/files/deno.ts

@@ -38,7 +38,7 @@ export class BIDSFileDeno implements BIDSFile {
     try {
       this.#fileInfo = Deno.statSync(this._getPath())
     } catch (error) {
-      if (error.code === 'ENOENT') {
+      if (error && typeof error === 'object' && 'code' in error && error.code === 'ENOENT') {
         this.#fileInfo = Deno.lstatSync(this._getPath())
       }
     }
@@ -158,7 +158,7 @@ export async function readFileTree(rootPath: string): Promise<FileTree> {
     )
     ignore.add(await readBidsIgnore(ignoreFile))
   } catch (err) {
-    if (!Object.hasOwn(err, 'code') || err.code !== 'ENOENT') {
+    if (err && typeof err === 'object' && !('code' in err && err.code !== 'ENOENT')) {
       logger.error(`Failed to read '.bidsignore' file with the following error:\n${err}`)
     }
   }

bids-validator/src/files/inheritance.test.ts

@@ -1,4 +1,4 @@
-import { assertEquals, assertThrows } from '@std/assert'
+import { assert, assertEquals, assertThrows } from '@std/assert'
 import { pathsToTree } from './filetree.ts'
 import { walkBack } from './inheritance.ts'
 
@@ -17,6 +17,9 @@ Deno.test('walkback inheritance tests', async (t) => {
           continue
         }
       } catch (error) {
+        assert(error)
+        assert(typeof error === 'object')
+        assert('code' in error)
         assertEquals(error.code, 'MULTIPLE_INHERITABLE_FILES')
         throw error
       }

bids-validator/src/schema/associations.ts

@@ -163,7 +163,8 @@
     try {
       file = walkBack(source, inherit, extensions, suffix).next().value
     } catch (error) {
-      if (error.code === 'MULTIPLE_INHERITABLE_FILES') {
+      if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') {
+        // @ts-expect-error
         issues.add(error)
         break
       } else {

bids-validator/src/schema/context.ts

@@ -184,7 +184,8 @@
     try {
       sidecars = [...walkBack(this.file)]
     } catch (error) {
-      if (error.code === 'MULTIPLE_INHERITABLE_FILES') {
+      if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') {
+        // @ts-expect-error
         this.dataset.issues.add(error)
       } else {
         throw error

bids-validator/src/utils/errors.ts

@@ -1,5 +1,6 @@
 export class SchemaStructureError extends Error {
-  constructor(schemaPath) {
+  schemaPath: string
+  constructor(schemaPath: string) {
     super(`Validator attempted to access ${schemaPath}, but it wasn't there.`)
     this.name = 'SchemaStructureError'
     this.schemaPath = schemaPath

bids-validator/src/validators/hed.ts

@@ -80,7 +80,7 @@ export async function hedValidate(
     context.dataset.issues.add({
       code: 'HED_ERROR',
       location: context.path,
-      issueMessage: error,
+      issueMessage: error as string,
     })
   }
 

bids-validator/src/version.ts

@@ -32,13 +32,12 @@ export async function getVersion(): Promise<string> {
 }
 
 async function getLocalVersion(path: string): Promise<string> {
-  const p = Deno.run({
-    // safe.directory setting so we could still operate from another user
-    cmd: ['git', '-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'],
-    stdout: 'piped',
+  // safe.directory setting so we could still operate from another user
+  const command = new Deno.Command("git", {
+    args: ['git', '-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'],
   })
-  const description = new TextDecoder().decode(await p.output()).trim()
-  p.close()
+  const { success, stdout } = await command.output();
+  const description = new TextDecoder().decode(stdout).trim()
   return description
 }