Merge pull request #2176 from effigies/fix/blacklist-inputs

fix(cli): Allow blacklisting any modality from schema.rules.modalities

Author: rwblair

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}`)
       }
     }
   }