From c08b410373c56ffc3a8ea61dc8f6a898a52cef45 Mon Sep 17 00:00:00 2001
From: Brandon Rose <rose.brandon.m@gmail.com>
Date: Tue, 31 Mar 2026 12:34:41 -0500
Subject: [PATCH] Fix kernel permission error by running Jupyter server as
 jupyter user instead of root

---
 Dockerfile          |  3 +++
 docker-compose.yaml | 30 +++++++++++++++---------------
 2 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 052e104..2e38774 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -71,5 +71,8 @@ ENV BEAKER_AGENT_USER=jupyter \
     BEAKER_RUN_PATH=/var/run/beaker \
     BEAKER_APP=biome.app.BiomeApp
 
+# Run as jupyter user
+USER jupyter
+
 # Service
 CMD ["python", "-m", "beaker_kernel.service.server", "--ip", "0.0.0.0"]
\ No newline at end of file
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 0084652..772d46f 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -34,21 +34,21 @@ services:
       - ./literature_review:/jupyter/_literature_review
     networks:
       - beaker
-  rest_api:
-    build:
-      context: .
-      dockerfile: ./rest_api/Dockerfile
-    volumes:
-      - ./adhoc_data:/jupyter/integrations
-    env_file:
-      - .env
-    ports:
-      - "8001:8001"
-    environment:
-      - BIOME_INTEGRATIONS_DIR=/integrations
-      - BIOME_DATA_DIR=/data
-    networks:
-      - beaker
+  # rest_api:
+  #   build:
+  #     context: .
+  #     dockerfile: ./rest_api/Dockerfile
+  #   volumes:
+  #     - ./adhoc_data:/jupyter/integrations
+  #   env_file:
+  #     - .env
+  #   ports:
+  #     - "8001:8001"
+  #   environment:
+  #     - BIOME_INTEGRATIONS_DIR=/integrations
+  #     - BIOME_DATA_DIR=/data
+  #   networks:
+  #     - beaker
   # ui:
   #   image: node:20
   #   user: "node"