From 37ff18c3a14f224c08abd3e593d6074941c9e803 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 16 Sep 2025 15:35:18 -0500
Subject: [PATCH 1/2] First pass at patching schema on load with file passed to
 cli.

---
 src/setup/loadSchema.ts | 28 +++++++++++++++++++++++++++-
 src/setup/options.ts    |  5 +++++
 src/validators/bids.ts  |  2 +-
 3 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/src/setup/loadSchema.ts b/src/setup/loadSchema.ts
index d8b45f56f..1ae8ae0c2 100644
--- a/src/setup/loadSchema.ts
+++ b/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
 }
diff --git a/src/setup/options.ts b/src/setup/options.ts
index 0c58b1291..3d32540c3 100644
--- a/src/setup/options.ts
+++ b/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') {
diff --git a/src/validators/bids.ts b/src/validators/bids.ts
index 32e57efb3..cdc897958 100644
--- a/src/validators/bids.ts
+++ b/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

From bc745d7692591e70eb085135e0476482cb5f6bbe Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Tue, 16 Sep 2025 15:42:11 -0500
Subject: [PATCH 2/2] add print flag. Need to figure out how to make
 datasetPath optional when its used...

---
 src/setup/loadSchema.ts | 6 +++++-
 src/setup/options.ts    | 5 +++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/setup/loadSchema.ts b/src/setup/loadSchema.ts
index 1ae8ae0c2..b24072f67 100644
--- a/src/setup/loadSchema.ts
+++ b/src/setup/loadSchema.ts
@@ -27,7 +27,7 @@ function merge(obj1, obj2) {
  *
  * version is ignored when the network cannot be accessed
  */
-export async function loadSchema(version?: string, patch?: string): Promise<Schema> {
+export async function loadSchema(version?: string, patch?: string, print?: boolean): Promise<Schema> {
   let schemaUrl = version
   const bidsSchema = typeof Deno !== 'undefined' ? Deno.env.get('BIDS_SCHEMA') : undefined
   if (bidsSchema !== undefined) {
@@ -64,6 +64,10 @@ export async function loadSchema(version?: string, patch?: string): Promise<Sche
     schema = merge(schema, patchJson)
   }
 
+  if (print) {
+    console.log(JSON.stringify(schema))
+    Deno.exit(0)
+  }
   setCustomMetadataFormats(schema)
   return schema
 }
diff --git a/src/setup/options.ts b/src/setup/options.ts
index 3d32540c3..3a0c62d22 100644
--- a/src/setup/options.ts
+++ b/src/setup/options.ts
@@ -33,6 +33,7 @@ export type ValidatorOptions = {
   prune?: boolean
   maxRows?: number
   schemaAddon?: string
+  printSchema?: boolean
 }
 
 const datasetType = new EnumType<string>(
@@ -103,6 +104,10 @@ export const validateCommand: Command<void, void, any, string[], void> = new Com
     '--schema-addon <file:string>',
     'Json file to be merged with loaded schema.',
   )
+  .option(
+    '--printSchema',
+    'Print schema that was loaded and exit.',
+  )
 
 // Disabling color output is only available in Deno
 if (typeof Deno !== 'undefined') {