First pass at patching schema on load with file passed to cli.

Author: rwblair

src/setup/loadSchema.ts

@@ -3,12 +3,31 @@ import { objectPathHandler } from '../utils/objectPathHandler.ts'
 import { schema as schemaDefault } from '@bids/schema'
 import { setCustomMetadataFormats } from '../validators/json.ts'
 
+function merge(obj1, obj2) {
+  if (Array.isArray(obj1) && Array.isArray(obj2)) {
+    return [...obj1, ...obj2]
+  }
+
+  let  merged = obj1
+  if (typeof obj1 !== "object" || typeof obj2 !== "object") {
+    return merged
+  }
+  Object.keys(obj2).map(key => {
+    if (key in obj1) {
+      merged[key] = merge(obj1[key], obj2[key])
+    } else {
+      merged[key] = obj2[key]
+    }
+  })
+  return merged
+}
+
 /**
  * Load the schema from the specification
  *
  * version is ignored when the network cannot be accessed
  */
-export async function loadSchema(version?: string): Promise<Schema> {
+export async function loadSchema(version?: string, patch?: string): Promise<Schema> {
   let schemaUrl = version
   const bidsSchema = typeof Deno !== 'undefined' ? Deno.env.get('BIDS_SCHEMA') : undefined
   if (bidsSchema !== undefined) {
@@ -38,6 +57,13 @@ export async function loadSchema(version?: string): Promise<Schema> {
       )
     }
   }
+
+  if (patch) {
+    let patchText = await Deno.readTextFile(patch);
+    let patchJson = JSON.parse(patchText)
+    schema = merge(schema, patchJson)
+  }
+
   setCustomMetadataFormats(schema)
   return schema
 }

src/setup/options.ts

@@ -32,6 +32,7 @@ export type ValidatorOptions = {
   blacklistModalities: string[]
   prune?: boolean
   maxRows?: number
+  schemaAddon?: string
 }
 
 const datasetType = new EnumType<string>(
@@ -98,6 +99,10 @@ export const validateCommand: Command<void, void, any, string[], void> = new Com
     '-o, --outfile <file:string>',
     'File to write validation results to.',
   )
+  .option(
+    '--schema-addon <file:string>',
+    'Json file to be merged with loaded schema.',
+  )
 
 // Disabling color output is only available in Deno
 if (typeof Deno !== 'undefined') {

src/validators/bids.ts

@@ -46,7 +46,7 @@ export async function validate(
   config?: Config,
 ): Promise<ValidationResult> {
   const summary = new Summary()
-  const schema = await loadSchema(options.schema)
+  const schema = await loadSchema(options.schema, options?.schemaAddon)
   summary.schemaVersion = schema.schema_version
 
   /* There should be a dataset_description in root, this will tell us if we