From b8d5490675a8fa9f71ad0bd151227a162f00f1ad Mon Sep 17 00:00:00 2001
From: Scott Christley <scott.christley@utsouthwestern.edu>
Date: Mon, 12 Feb 2024 21:21:04 -0600
Subject: [PATCH] merge allOfs as dereference does not

---
 lang/js/airr.js      | 13 +++++++++++++
 lang/js/package.json |  1 +
 2 files changed, 14 insertions(+)

diff --git a/lang/js/airr.js b/lang/js/airr.js
index e34fdeae0..09857b531 100644
--- a/lang/js/airr.js
+++ b/lang/js/airr.js
@@ -17,6 +17,7 @@ var yaml = require('js-yaml');
 var path = require('path');
 var fs = require('fs');
 const $RefParser = require("@apidevtools/json-schema-ref-parser");
+const merge = require('allof-merge');
 
 var airr = {};
 module.exports = airr;
@@ -30,6 +31,12 @@ airr.load_schema = async function() {
 
     // dereference all $ref objects
     var spec = await $RefParser.dereference(doc);
+    // merge allOfs
+    for (let obj in spec) {
+        if (spec[obj]['type'] || spec[obj]['allOf']) {
+            spec[obj] = merge.merge(spec[obj]);
+        }
+    }
     var schema = require('./schema')(airr, spec);
     var io = require('./io')(airr);
 
@@ -45,6 +52,12 @@ airr.load_custom_schema = async function(obj, filename) {
 
     // dereference all $ref objects
     var spec = await $RefParser.dereference(doc);
+    // merge allOfs
+    for (let obj in spec) {
+        if (spec[obj]['type'] || spec[obj]['allOf']) {
+            spec[obj] = merge.merge(spec[obj]);
+        }
+    }
     var schema = require('./schema')(obj, spec);
 
     return Promise.resolve(spec);
diff --git a/lang/js/package.json b/lang/js/package.json
index 29b889986..e80c567d4 100644
--- a/lang/js/package.json
+++ b/lang/js/package.json
@@ -25,6 +25,7 @@
     "@apidevtools/json-schema-ref-parser": "^10.1.0",
     "ajv": "^8.12.0",
     "ajv-formats": "^2.1.1",
+    "allof-merge": "^0.6.5",
     "csv-parser": "^2.3.2",
     "js-yaml": "^3.10.0"
   },