Merge remote-tracking branch 'origin/master' into fix/deno_2_test_and_build

Author: rwblair

.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:

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": [

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/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

bids-validator/src/main.ts

@@ -8,6 +8,7 @@ import { validate } from './validators/bids.ts'
 import { consoleFormat, resultToJSONStr } from './utils/output.ts'
 import { setupLogging } from './utils/logger.ts'
 import type { ValidationResult } from './types/validation-result.ts'
+export type { ValidationResult } from './types/validation-result.ts'
 
 /**
  * Validation entrypoint intended for command line usage with Deno

bids-validator/src/setup/options.ts

@@ -3,6 +3,7 @@ import type { LevelName } from '@std/log'
 import { Command, EnumType } from '@cliffy/command'
 import { getVersion } from '../version.ts'
 import type { Issue, Severity } from '../types/issues.ts'
+import { schema } from '@bids/schema'
 
 /**
  * BIDS Validator config file object definition
@@ -31,7 +32,7 @@ export type ValidatorOptions = {
 }
 
 const modalityType = new EnumType<string>(
-  ['MRI', 'PET', 'MEG', 'EEG', 'iEEG', 'Microscopy', 'NIRS', 'MRS'],
+  Object.keys(schema.rules.modalities)
 )
 
 /** Extendable Cliffy Command with built in BIDS validator options */

bids-validator/src/validators/bids.ts

@@ -18,6 +18,7 @@ import { type BIDSContext, BIDSContextDataset } from '../schema/context.ts'
 import type { parseOptions } from '../setup/options.ts'
 import { hedValidate } from './hed.ts'
 import { citationValidate } from './citation.ts'
+import { logger } from '../utils/logger.ts'
 
 /**
  * Ordering of checks to apply
@@ -121,8 +122,12 @@ export async function validate(
     // 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 (datatypes) {
+        for (const datatype of datatypes) {
+          blacklistedDatatypes.set(datatype, modality)
+        }
+      } else {
+        logger.warn(`Attempted to blacklist unknown modality: ${modality}`)
       }
     }
   }