Added a lot of robustness features to the scripts

.gitignore

@@ -0,0 +1,2 @@
+
+*.log

README.md

@@ -2,6 +2,19 @@
 
 This repository contains convenience scripts for installing vantage6 nodes at data stations participating in the BLUEBERRY project.
 
+## TODO
+
+- [ ] Fix the `$SCRIPT_DIR` variable
+- [ ] SSH Key is not set as this is computed in a subshell
+- [ ] Miniconda seems to install every time
+- [ ] `Bash` session is not invoked after installation (manual step?)
+- [ ] Start the node after installation
+- [ ] Add `start-node.sh` and `stop-node.sh` scripts
+- [ ] Add a job to the crontab to start the node on boot
+- [ ] Connect to `cotopaxi.vantage6.ai` to test
+- [ ] Add option to use Docker version of the OMOP database (no SSH tunneling required)
+- [ ] Finish `create-node.sh` script
+
 ## Getting Started
 
 These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

create-node.sh

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+#! /bin/bash
+
+source ./utils.sh
+
+# Create config dir
+print_step "Creating config dir"
+mkdir -p ~/.config
+
+# Create config file
+print_step "Creating config file"
+echo "  - Please enter the API key:"
+read API_KEY
+
+# vantage6 node settings
+export API_KEY=$API_KEY
+export TASK_DIR=$HOME/tasks
+
+mkdir -p $TASK_DIR
+
+# OMOP settings
+export OMOP_HOST="omop"
+export OMOP_PORT=5432
+
+# TODO @biomeris which settings?
+export OMOP_DATABASE="postgres"
+export OMOP_USER="postgres"
+export OMOP_PASSWORD="postgres"
+export OMOP_CDM_SCHEMA="cmd"
+export OMOP_RESULT_SCHEMA="result"
+
+# Check if the vantage6-node user already exists
+print_step "Checking if the vantage6-node user already exists"
+NEW_USER="vantage6-node"
+if id -u "vantage6-node" >/dev/null 2>&1; then
+    print_step "The vantage6-node user already exists"
+else
+    print_step "Creating new user"
+    sudo useradd $NEW_USER
+
+    # Set password for the new user
+    PASSWORD=$(openssl rand -base64 16)
+    echo $PASSWORD | sudo passwd --stdin $NEW_USER
+fi
+
+
+print_step "Executing some steps as the $NEW_USER user"
+# Run the create_ssh_key.sh script as the new user
+# sudo -u $NEW_USER bash -c "./create_ssh_user.sh" | tee /dev/stdout
+print_step "Changing back to the original user"
+
+# Tunnel settings
+print_step "Setting tunnel settings"
+# export TUNNEL_HOSTNAME=$OMOP_HOST
+# export SSH_HOST=$(hostname -I | awk '{print $1}')
+# print_step "SSH_HOST: $SSH_HOST"
+# export SHH_PORT=22
+# export SSH_HOST_FINGERPRINT=$(cat /etc/ssh/ssh_host_rsa_key.pub)
+
+# export SSH_USERNAME=$NEW_USER
+# export SSH_KEY=$PRIVATE_KEY_FILE
+
+# export TUNNEL_BIND_IP="0.0.0.0"
+# export TUNNEL_BIND_PORT=$OMOP_PORT
+
+# export TUNNEL_REMOTE_IP="127.0.0.1"
+# export TUNNEL_REMOTE_PORT=5432
+
+# # Create the config file
+print_step "Creating the config file"
+# print_step $USER
+# mkdir -p ~/.config/vantage6/node
+# envsubst < ./v6-blueberry-installation-scripts/node.tpl > $HOME/.config/vantage6/node/blueberry.yml
+# cat << EOF > ~/.config/vantage6/node/config.yml
+
+

create-ssh-user.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Switch to the new user's home directory
+cd ~
+
+# Generate a new SSH key pair
+echo "Generating a new SSH key pair"
+mkdir -p ~/.ssh
+PRIVATE_KEY_FILE="~/.ssh/id_rsa"
+ssh-keygen -t rsa -b 4096 -f $PRIVATE_KEY_FILE -N ""
+
+# Add the public key to the authorized_keys file
+echo "Adding the public key to the authorized_keys file"
+PUBLIC_KEY=$(cat $PRIVATE_KEY_FILE.pub)
+touch ~/.ssh/authorized_keys
+echo $PUBLIC_KEY >> ~/.ssh/authorized_keys
+
+# Set the correct permissions
+echo "Setting the correct permissions"
+chmod 700 ~/.ssh
+chmod 600 ~/.ssh/authorized_keys
+chmod 600 ~/.ssh/id_rsa
+chmod 644 ~/.ssh/id_rsa.pub

install-all.sh

@@ -1,10 +1,27 @@
 #!/bin/bash
 
+source ./utils.sh
+print_intro
+confirm_or_exit
+
+# Update the current system
+print_header "Updating the current system"
+sudo dnf update -y &>> update-system.log
+
 # Run the install-docker.sh script
-bash install-docker.sh
+print_header "Installing Docker"
+source ./install-docker.sh
 
 # Run the install-miniconda.sh script
-bash install-miniconda.sh
+print_header "Installing Miniconda"
+source ./install-miniconda.sh
 
 # Run the install-vantage6.sh script
-bash install-vantage6.sh
+print_header "Installing vantage6"
+source ./install-vantage6.sh
+
+# Configure the vantage6-node
+print_header "Creating vantage6-node"
+source ./create-node.sh
+
+print_outro

install-docker.sh

@@ -1,29 +1,51 @@
 #!/bin/bash
 
 # Print the current time and user
-echo "Current time: $(date)" &>> docker-install.log
-echo "Current user: $(whoami)" &>> docker-install.log
-
-# Update the apt package index
-sudo yum update -y &>> docker-install.log
-
-# Install necessary packages
-sudo yum install -y yum-utils &>> docker-install.log
-
-# Set up the stable repository
-sudo yum-config-manager --add-repo https://download.docker.com/linux/oracle/docker-ce.repo &>> docker-install.log
-
-# Install the latest version of Docker Engine and containerd
-sudo yum install -y docker-ce docker-ce-cli containerd.io &>> docker-install.log
-
-# Start Docker
-sudo systemctl start docker &>> docker-install.log
-
-# Enable Docker to start on boot
-sudo systemctl enable docker &>> docker-install.log
-
-# Add the current user to the docker group
-sudo usermod -aG docker $USER &>> docker-install.log
-
-# Apply the new group membership to the current session
-newgrp docker &>> docker-install.log
+source ./utils.sh
+print_info &>> docker-install.log
+
+print_step "Checking if Docker is already installed"
+if command -v docker &> /dev/null
+then
+    print_step "Docker is already installed" | tee -a docker-install.log
+else
+
+    # Update the apt package index
+    print_step "Updating the current system"
+    sudo dnf update -y &>> docker-install.log
+
+    # Install necessary packages
+    print_step "Installing necessary packages"
+    sudo dnf install -y dnf-utils &>> docker-install.log
+
+    # Set up the stable repository
+    print_step "Setting up the stable repository"
+    sudo dnf config-manager --add-repo=https://download.docker.com/linux/centos/docker-ce.repo &>> docker-install.log
+
+    # Install the latest version of Docker Engine and containerd
+    print_step "Installing Docker"
+    sudo dnf install docker-ce --nobest -y &>> docker-install.log
+
+    # Start Docker
+    print_step "Starting Docker"
+
+    # Enable Docker to start on boot
+    print_step "Enabling Docker to start on boot & start Docker"
+    if command -v systemctl &> /dev/null
+    then
+        sudo systemctl enable docker &>> docker-install.log
+        sudo systemctl start docker
+    else
+        print_warning "Systemctl not found, are you testing?"
+        print_warning "If not, docker will not start automatically on boot"
+        sudo service docker start
+    fi
+
+    # Add the current user to the docker group
+    print_step "Adding the current user '$USER' to the docker group"
+    sudo usermod -aG docker $USER &>> docker-install.log
+
+    # Apply the new group membership to the current session
+    print_step "Applying the new group membership to the current session"
+    newgrp docker &>> docker-install.log
+fi

install-miniconda.sh

@@ -1,14 +1,27 @@
 #!/bin/bash
 
 # Print the current time and user
-echo "Current time: $(date)" &>> miniconda-install.log
-echo "Current user: $(whoami)" &>> miniconda-install.log
+source ./utils.sh
+print_info &>> miniconda-install.log
 
-# Download the Miniconda installer script
-curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &>> miniconda-install.log
+# Check if Miniconda is already installed
+print_step "Checking if Miniconda is already installed"
+if command -v conda &> /dev/null; then
+    print_step "Miniconda is already installed." | tee -a miniconda-install.log
+else
+    # Download the Miniconda installer script
+    print_step "Downloading the Miniconda installer script"
+    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &>> miniconda-install.log
 
-# Run the installer script
-bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda &>> miniconda-install.log
+    # Run the installer script
+    print_step "Running the Miniconda installer script"
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda &>> miniconda-install.log
 
-# Initialize Miniconda to automatically update the PATH
-$HOME/miniconda/bin/conda init &>> miniconda-install.log
+    # Initialize Miniconda to automatically update the PATH
+    print_step "Initializing Miniconda to automatically update the PATH"
+    $HOME/miniconda/bin/conda init &>> miniconda-install.log
+
+    # Activate the base environment
+    print_step "Activating the base environment"
+    source ~/.bashrc
+fi

install-vantage6.sh

@@ -1,8 +1,44 @@
-# Create a new conda environment with Python 3.10
-$HOME/miniconda/bin/conda create -n vantage6 python=3.10 -y &>> vantage6-install.log
+#!/bin/bash
+
+# Print the current time and user
+source ./utils.sh
+print_info &>> vantage6-install.log
+
+# Check if the vantage6 environment already exists
+print_step "Checking if the vantage6 environment already exists"
+if conda env list | grep -q 'vantage6'
+then
+    print_step "The vantage6 environment already exists" | tee -a vantage6-install.log
+else
+    # Create a new conda environment with Python 3.10
+    print_step "Creating a new conda environment with Python 3.10"
+    conda create -n vantage6 python=3.10 -y &>> vantage6-install.log
+fi
 
 # Activate the new environment
-$HOME/miniconda/bin/activate vantage6 &>> vantage6-install.log
+print_step "Activating the (new) environment"
+conda activate vantage6 &>> vantage6-install.log
 
 # Install the vantage6 package
-pip install vantage6 &>> vantage6-install.log
+print_step "Checking if the vantage6 package is already installed"
+if pip freeze | grep -q 'vantage6=='
+then
+    # Print the version of the vantage6 package
+    print_step "The vantage6 package is already installed" | tee -a vantage6-install.log
+    vantage6_version=$(pip show vantage6 | grep Version | cut -d ' ' -f 2)
+    print_step "vantage6 version: $vantage6_version" | tee -a vantage6-install.log
+
+    # Ask for confirmation to upgrade the vantage6 package
+    if confirm "Do you want to try to upgrade the vantage6 package?"
+    then
+        print_step "Upgrading the vantage6 package"
+        pip install --upgrade vantage6 &>> vantage6-install.log
+    fi
+else
+    # Install the vantage6 package
+    print_step "Installing the vantage6 package"
+    pip install vantage6 &>> vantage6-install.log
+fi
+
+vantage6_version=$(pip show vantage6 | grep Version | cut -d ' ' -f 2)
+print_step "vantage6 version: $vantage6_version" | tee -a vantage6-install.log