Merge pull request #195 from nmfs-opensci/eeholmes-patch-1

export PATH in scripts that switch to NB_USER

scripts/install-conda-packages.sh

@@ -18,6 +18,8 @@ ENV_NAME="${2:-${CONDA_ENV}}"
 # Check if running as root and switch to NB_USER if needed
 if [[ $(id -u) -eq 0 ]]; then
     echo "Switching to ${NB_USER} to run install-conda-packages.sh"
+    # Be aware that the next line is resetting PATH to not include conda bins. If this becomes a problem, uncomment the following
+    # export PATH="$PATH"
     exec su "${NB_USER}" -c "/bin/bash $0 $ENV_FILE $ENV_NAME"
 fi
 

scripts/install-desktop.sh

@@ -1,20 +1,20 @@
 #!/bin/bash
 # Required User: root
-# Usage: RUN /pyrocket_scripts/setup-desktop.sh <directory path>"
+# Usage: RUN /pyrocket_scripts/install-desktop.sh <directory path>"
 
 echo "Running setup-desktop.sh"
 
 # Check if the script is run as root
 if [[ $(id -u) -ne 0 ]]; then
-    echo "  Error: This script must be run as root. Please use 'USER root' in your Dockerfile before running this script."
+    echo "  Error: This install-desktop.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
 
 # Check if a directory argument is provided
 if [ -z "$1" ]; then
     echo "  Error: No directory provided. Please provide a directory path where the script can find .desktop, .png, and .xml files."
-    echo "  Usage: RUN /pyrocket_scripts/setup-desktop.sh <directory path>"
+    echo "  Usage: RUN /pyrocket_scripts/install-desktop.sh <directory path>"
     exit 1
 fi
 
@@ -40,17 +40,17 @@ find "${TARGET_DIR}" -type f \( -name "*.desktop" -o -name "*.png" -o -name "*.x
 if [ "$(ls -A "${REPO_DIR}/Desktop" 2>/dev/null)" ]; then
     echo "  Successfully copied Desktop-related files to '${REPO_DIR}/Desktop'."
 else
-    echo "  Warning: No .desktop, .png, or .xml files found in '${TARGET_DIR}'. Nothing was copied."
+    echo "  Warning: No .desktop, .png, or .xml files found in '${TARGET_DIR}'. Skipping installation."
+    exit 0  # Exit without error if no files were found
 fi
 
 # Check if desktop.sh exists before executing
 if [ -f "${REPO_DIR}/scripts/setup-desktop.sh" ]; then
     echo "  Running ${REPO_DIR}/scripts/setup-desktop.sh to move Desktop files to appropriate directories and register as applications."
     chmod +x "${REPO_DIR}/scripts/setup-desktop.sh"
     "${REPO_DIR}/scripts/setup-desktop.sh"
+    echo "  Success! install-desktop.sh Desktop files installed."
 else
-    echo "  Warning: ${REPO_DIR}/scripts/setup-desktop.sh not found. Skipping execution."
+    echo "  Error: ${REPO_DIR}/scripts/setup-desktop.sh not found. This script is required for Desktop application installation."
+    exit 1
 fi
-
-echo "  Success! install-desktop.sh"
-

scripts/install-pip-packages.sh

@@ -11,6 +11,8 @@ fi
 # Check if running as root and switch to NB_USER if needed
 if [[ $(id -u) -eq 0 ]]; then
     echo "Switching to ${NB_USER} to run install-pip-packages.sh"
+    # Be aware that the next line is resetting PATH to not include conda bins. If this becomes a problem, uncomment the following
+    # export PATH="$PATH"
     exec su "${NB_USER}" -c "/bin/bash $0 $1"  # Pass along the filename argument
 fi
 

scripts/setup-desktop.sh

@@ -1,10 +1,18 @@
 #!/bin/bash
+# Required user: root
 # The default for XDG and xfce4 is for Desktop files to be in ~/Desktop but this leads to a variety of problems
 # First we are altering the user directiory which seems rude, second orphan desktop files might be in ~/Desktop so who knows
 # what the user Desktop experience with be, here the Desktop dir is set to /usr/share/Desktop so is part of the image.
 # users that want to customize Desktop can change /etc/xdg/user-dirs.dirs though py-rocket resets that each time the server is restarted.
 set -e
 
+# Check if the script is run as root
+if [[ $(id -u) -ne 0 ]]; then
+    echo "  Error: This setup-desktop.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
+
 # Copy in the Desktop files
 APPLICATIONS_DIR=/usr/share/applications/packages
 DESKTOP_DIR=/usr/share/Desktop

scripts/setup-start.sh

@@ -11,6 +11,8 @@ fi
 # Check if running as root and switch to NB_USER if needed
 if [[ $(id -u) -eq 0 ]]; then
     echo "Switching to ${NB_USER} to run setup-start.sh"
+    # Be aware that the next line is resetting PATH to not include conda bins. If this becomes a problem, uncomment the following
+    # export PATH="$PATH"
     exec su "${NB_USER}" -c "/bin/bash $0 $1"  # Pass the script file as an argument
 fi