Merge pull request #2106 from nellh/2105-xml2js-fix

fix: Use @libs/xml over xml2js for tiff parsing

.github/workflows/deno_tests.yml

@@ -27,6 +27,7 @@ jobs:
           deno-version: v1.x
       - run: ./build.ts
         working-directory: ./bids-validator
+      - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version
       - uses: actions/upload-artifact@v4
         with:
           name: main

bids-validator/deno.json

@@ -34,7 +34,7 @@
     "@hed/validator": "npm:[email protected]",
     "@ignore": "npm:[email protected]",
     "@mango/nifti": "npm:[email protected]",
-    "@xml2js": "npm:[email protected]"
+    "@libs/xml": "jsr:@libs/[email protected]"
   },
   "tasks": {
     "test": "deno test -A src/tests/"

bids-validator/src/files/tiff.ts

@@ -3,7 +3,7 @@
  * Module for extracting Tiff metadata
  */
 import { Ome, Tiff } from '@bids/schema/context'
-import * as xml2js from '@xml2js'
+import * as XML from '@libs/xml'
 import { BIDSFile } from '../types/filetree.ts'
 
 function getImageDescription(
@@ -57,19 +57,19 @@ export async function parseTIFF(
   }
 
   const imageDescription = getImageDescription(dataview, littleEndian, version === 42 ? 12 : 20)
-  const omexml = await xml2js.parseStringPromise(imageDescription || '') as { [key: string]: any }
-  const Pixels = omexml?.OME?.Image[0]?.Pixels[0]["$"]
+  const omexml = await XML.parse(imageDescription || '') as { [key: string]: any }
+  const Pixels = omexml?.OME?.Image?.Pixels
   if (!Pixels) return { tiff: { version } }
 
   return {
     tiff: { version },
     ome: {
-      PhysicalSizeX: parseFloat(Pixels['PhysicalSizeX']),
-      PhysicalSizeY: parseFloat(Pixels['PhysicalSizeY']),
-      PhysicalSizeZ: parseFloat(Pixels['PhysicalSizeZ']),
-      PhysicalSizeXUnit: Pixels['PhysicalSizeXUnit'],
-      PhysicalSizeYUnit: Pixels['PhysicalSizeYUnit'],
-      PhysicalSizeZUnit: Pixels['PhysicalSizeZUnit'],
+      PhysicalSizeX: parseFloat(Pixels['@PhysicalSizeX']),
+      PhysicalSizeY: parseFloat(Pixels['@PhysicalSizeY']),
+      PhysicalSizeZ: parseFloat(Pixels['@PhysicalSizeZ']),
+      PhysicalSizeXUnit: Pixels['@PhysicalSizeXUnit'],
+      PhysicalSizeYUnit: Pixels['@PhysicalSizeYUnit'],
+      PhysicalSizeZUnit: Pixels['@PhysicalSizeZUnit'],
     },
   }
 }

bids-validator/src/validators/bids.ts

@@ -108,11 +108,13 @@ export async function validate(
 
   const modalitiesRule = schema.rules.modalities as Record<string, { datatypes: string[] }>
   const blacklistedDatatypes = new Map<string, string>()
-  // Map blacklisted datatypes back to the modality that generated them
-  for (const modality of options.blacklistModalities) {
-    const datatypes = modalitiesRule[modality.toLowerCase()]?.datatypes as string[]
-    for (const datatype of datatypes) {
-      blacklistedDatatypes.set(datatype, modality)
+  if (options.blacklistModalities) {
+    // Map blacklisted datatypes back to the modality that generated them
+    for (const modality of options.blacklistModalities) {
+      const datatypes = modalitiesRule[modality.toLowerCase()]?.datatypes as string[]
+      for (const datatype of datatypes) {
+        blacklistedDatatypes.set(datatype, modality)
+      }
     }
   }
 

web/vite.config.mts

@@ -6,10 +6,27 @@ import { nodePolyfills } from "npm:[email protected]"
 import "npm:react@^18.2.0"
 import "npm:react-dom@^18.2.0"
 
+/**
+ * Vite plugin to hack a bug injected by the default assetImportMetaUrlPlugin
+ */
+function workaroundAssetImportMetaUrlPluginBug() {
+  return {
+    name: "vite-workaround-import-glob",
+    transform(src, id) {
+      if (id.includes('validator/main.js')) {
+        return src.replace(", import.meta.url", "")
+      } else {
+        return null
+      }
+    }
+  }
+}
+
 // https://vitejs.dev/config/
 export default defineConfig({
   base: '',
   plugins: [
+    workaroundAssetImportMetaUrlPluginBug(),
     httpsImports.default(),
     react(),
     nodePolyfills({