From 2bb33c01c9e82b4fd3a9a02455abb3934e4423dc Mon Sep 17 00:00:00 2001
From: Trey Chadick <tchad@labkey.com>
Date: Fri, 19 Dec 2025 11:37:05 -0800
Subject: [PATCH] Specify source root for CodeQL initialization

---
 .github/workflows/codeql.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 0b4330414..3042d6dde 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -46,7 +46,7 @@ jobs:
         - language: actions
           build-mode: none
         - language: java-kotlin
-          build-mode: manual # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
+          build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
         - language: javascript-typescript
           build-mode: none
         # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
@@ -80,6 +80,7 @@ jobs:
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v4
       with:
+        source-root: server/modules/commonAssays
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
         # If you wish to specify custom queries, you can do so here or in a config file.