Merge pull request #199 from nmfs-opensci/eeholmes-patch-2

fix home/jovyan permissions

Dockerfile

@@ -58,6 +58,9 @@ RUN mkdir -p ${XDG_CONFIG_HOME} && \
     chmod +x ${REPO_DIR}/scripts/setup-desktop.sh && \
     ${REPO_DIR}/scripts/setup-desktop.sh
 
+# Fix home permissions. Not needed in JupyterHub with persistent memory but needed if not used in that context
+RUN /pyrocket_scripts/fix-home-permissions.sh
+
 # Set up the start command 
 USER ${NB_USER}
 RUN chmod +x ${REPO_DIR}/start \

scripts/fix-home-permissions.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+# Required User: root
+
+echo "Running fix-home-permissions.sh"
+
+# Check if the script is run as root
+if [[ $(id -u) -ne 0 ]]; then
+    echo "Error: fix-home-permissions.sh must be run as root. Please use 'USER root' in your Dockerfile before running this script."
+    echo "Remember to switch back to the non-root user with 'USER ${NB_USER}' after running this script."
+    exit 1
+fi
+
+echo "Running fix-home-permissions.sh as $(whoami)..."
+
+# Define the target directory
+TARGET_DIR="/home/${NB_USER}"
+
+# Change ownership only for items not owned by ${NB_USER}
+sudo find "${TARGET_DIR}" ! -user "${NB_USER}" -exec chown "${NB_USER}:${NB_USER}" {} \;
+
+# Set permissions on all directories: read, write, and execute for ${NB_USER}
+sudo find "${TARGET_DIR}" -type d -exec chmod 755 {} \;
+
+# Set permissions on all files: read and write for ${NB_USER}
+sudo find "${TARGET_DIR}" -type f -exec chmod 644 {} \;

scripts/install-vscode-extensions.sh

@@ -33,7 +33,7 @@ fi
 # Set the extensions directory to be the conda dir so that it persists
 # Create if it doesn't exist; make owner jovyan
 EXT_DIR="${NB_PYTHON_PREFIX}/share/code-server/extensions"
-install -o jovyan -g jovyan -m 755 -d "${EXT_DIR}"
+install -o ${NB_USER} -g ${NB_USER} -m 755 -d "${EXT_DIR}"
 
 # Install each extension listed in the file; skip empty lines or comments
 while IFS= read -r EXT; do