added many improvements and some helper functions

README.md

@@ -5,9 +5,9 @@ This repository contains convenience scripts for installing vantage6 nodes at da
 ## TODO
 
 - [ ] Autmaticaly after installation?
-- [ ] Add `start-node.sh` and `stop-node.sh` scripts
 - [ ] Add a job to the crontab to start the node on boot
 - [ ] Add option to use Docker version of the OMOP database (no SSH tunneling required)
+- [ ] Add check that we are indeed using the bash shell
 - [ ] Update this README
 
 ## Getting Started

attach.sh

@@ -0,0 +1,3 @@
+#! /bin/bash
+SCRIPT_DIR=$(realpath "$(dirname "$0")")
+source $SCRIPT_DIR/node.sh attach blueberry

create-cronjob.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Get the directory of the current script
+SCRIPT_DIR=$(dirname "$(realpath "$0")")
+source $SCRIPT_DIR/utils.sh
+
+# Add a cron job that runs the start.sh script at startup
+print_step "Adding cron job"
+if ! check_command "crontab"; then
+    print_error "Failed to add cron job."
+else
+    (crontab -l 2>/dev/null; echo "@reboot $SCRIPT_DIR/start.sh") | crontab -
+fi

create-node.sh

@@ -73,7 +73,7 @@ print_step "TUNNEL_REMOTE_PORT: $TUNNEL_REMOTE_PORT"
 # # Create the config file
 print_step "Creating the config file"
 mkdir -p $HOME/.config/vantage6/node
-CONFIG_FILE=$HOME/.config/vantage6/node/blueberry.yml
+CONFIG_FILE=$HOME/.config/vantage6/node/blueberry.yaml
 
 if [ -f "$HOME/.config/vantage6/node/blueberry.yml" ]; then
     print_warning "Config file already exists at $CONFIG_FILE"

create-ssh-user.sh

@@ -3,24 +3,26 @@
 source $SCRIPT_DIR/utils.sh
 
 # Generate a new SSH key pair
-NEW_USER_HOME=/home/$NEW_USER
-sudo mkdir -p $NEW_USER_HOME/.ssh
-PRIVATE_KEY_FILE=$NEW_USER_HOME/.ssh/id_rsa
+
+PRIVATE_KEY_FILE=$HOME/tunnel_id_rsa
+
 # we need to do this ugly as we do not have permissions to check if the file exists
-if sudo sh -c "[ ! -f \"$PRIVATE_KEY_FILE\" ]"; then
+if [ ! -f "$PRIVATE_KEY_FILE" ]; then
     print_step "$PRIVATE_KEY_FILE does not exist"
     print_step "Generating a new SSH key pair"
-    sudo ssh-keygen -t rsa -b 4096 -f $PRIVATE_KEY_FILE -N "" -C "$NEW_USER"
+    sudo ssh-keygen -t rsa -b 4096 -f $PRIVATE_KEY_FILE -N "" -C "vantage6-tunnel"
 else
     print_warning "SSH key already exists at $PRIVATE_KEY_FILE"
 fi
 
 # Add the public key to the authorized_keys file
-print_step "Adding the public key to the authorized_keys file"
+print_step "Adding the public key to the authorized_keys file of the SSH user"
+NEW_USER_HOME=/home/$NEW_USER
+sudo mkdir -p $NEW_USER_HOME/.ssh
 PUBLIC_KEY=$(sudo cat $PRIVATE_KEY_FILE.pub)
 sudo touch $NEW_USER_HOME/.ssh/authorized_keys
 if ! sudo grep -q "$PUBLIC_KEY" $NEW_USER_HOME/.ssh/authorized_keys; then
-    sudo echo $PUBLIC_KEY >> $NEW_USER_HOME/.ssh/authorized_keys
+    echo $PUBLIC_KEY | sudo tee -a $NEW_USER_HOME/.ssh/authorized_keys > /dev/null
 else
     print_warning "Public key already exists in the authorized_keys file"
 fi
@@ -29,8 +31,8 @@ fi
 print_step "Setting the correct file permissions"
 sudo chmod 700 $NEW_USER_HOME/.ssh
 sudo chmod 600 $NEW_USER_HOME/.ssh/authorized_keys
-sudo chmod 600 $NEW_USER_HOME/.ssh/id_rsa
-sudo chmod 644 $NEW_USER_HOME/.ssh/id_rsa.pub
+sudo chmod 777 $HOME/tunnel_id_rsa
+sudo chmod 644 $HOME/tunnel_id_rsa.pub
 
 # Change the owner to $NEW_USER
 print_step "Changing the owner of the files to $NEW_USER"

install-all.sh

@@ -30,4 +30,16 @@ source $SCRIPT_DIR/install-vantage6.sh
 print_header "Creating vantage6-node"
 source $SCRIPT_DIR/create-node.sh
 
+print_header "Post installation steps"
+if confirm "Do you want to create a cronjob to automatically start the vantage6-node on boot?"; then
+    source $SCRIPT_DIR/create-cronjob.sh
+fi
+
+if confirm "Do you want to start the vantage6-node now?"; then
+    source $SCRIPT_DIR/node.sh start blueberry
+fi
+
+
+
+
 print_outro

node.sh

@@ -0,0 +1,27 @@
+#! /bin/bash
+SCRIPT_DIR=$(realpath "$(dirname "$0")")
+COMMAND=$1
+NODE_NAME=$2
+
+source $SCRIPT_DIR/utils.sh
+
+print_header "$COMMAND the vantage6-node"
+print_step "Checking if conda is installed"
+if ! check_command "conda"; then
+    print_error "Did you run the installation script? Exiting..."
+    exit 1
+fi
+
+print_step "Checking if the vantage6 environment exists"
+if ! check_env "vantage6"; then
+    print_error "Did you run the installation script? Exiting..."
+    exit 1
+fi
+
+print_step "Activating the vantage6 environment"
+source $HOME/miniconda/etc/profile.d/conda.sh
+conda activate vantage6
+
+# start the node
+print_step "$COMMAND the $NODE_NAME node"
+vnode $COMMAND --name $NODE_NAME

node.tpl

@@ -53,6 +53,7 @@ databases:
 
   - label: omop
     uri: jdbc:postgresql://${OMOP_HOST}:${OMOP_PORT}/${OMOP_DATABASE}
+    type: omop
     # additional environment variables that are passed to the algorithm
     # containers (or their wrapper). This can be used to for usernames
     # and passwords for example. Note that these environment variables are
@@ -139,22 +140,21 @@ ssh-tunnels:
         username: ${SSH_USERNAME}
         key: ${SSH_KEY}
 
-      # Once the SSH connection is established, a tunnel is created to
-      # forward traffic from the local machine to the remote machine.
-      tunnel:
-
-        # The port and ip on the tunnel container. The ip is always
-        # 0.0.0.0 as we want the algorithm container to be able to
-        # connect.
-        bind:
-          ip: ${TUNNEL_BIND_IP}
-          port: ${TUNNEL_BIND_PORT}
-
-        # The port and ip on the remote machine. If the data source runs
-        # on this machine, the ip most likely is 127.0.0.1.
-        dest:
-          ip: ${TUNNEL_REMOTE_IP}
-          port: ${TUNNEL_REMOTE_PORT}
+    # Once the SSH connection is established, a tunnel is created to
+    # forward traffic from the local machine to the remote machine.
+    tunnel:
+
+      # The port and ip on the tunnel container. The ip is always
+      # 0.0.0.0 as we want the algorithm container to be able to
+      # connect.
+      bind:
+        ip: ${TUNNEL_BIND_IP}
+        port: ${TUNNEL_BIND_PORT}
+      # The port and ip on the remote machine. If the data source runs
+      # on this machine, the ip most likely is 127.0.0.1.
+      dest:
+        ip: ${TUNNEL_REMOTE_IP}
+        port: ${TUNNEL_REMOTE_PORT}
 
 # # Whitelist URLs and/or IP addresses that the algorithm containers are
 # # allowed to reach using the http protocol.
@@ -219,7 +219,6 @@ debug:
   # into debug mode
   proxy_server: false
 
-
 # directory where local task files (input/output) are stored
 task_dir: ${TASK_DIR}
 

start.sh

@@ -0,0 +1,3 @@
+#! /bin/bash
+SCRIPT_DIR=$(realpath "$(dirname "$0")")
+source $SCRIPT_DIR/node.sh start blueberry

stop.sh

@@ -0,0 +1,3 @@
+#! /bin/bash
+SCRIPT_DIR=$(realpath "$(dirname "$0")")
+source $SCRIPT_DIR/node.sh stop blueberry

utils.sh

@@ -67,13 +67,14 @@ print_outro(){
     echo ""
     echo "  conda activate vantage6"
     echo ""
-    echo "Make sure the OMOP database is running and listening on 127.0.0.1:5432 "
+    echo "Make sure the OMOP database is running and listening on $TUNNEL_REMOTE_IP:$TUNNEL_REMOTE_PORT "
     echo "before starting the vantage6-node."
     print_divider
 }
 
 confirm() {
-    read -p "  ? $1 (y/n) " response
+    echo -e -n "\e[32m  ? $1 (y/n) \e[0m"
+    read response
     case "$response" in
         [yY][eE][sS]|[yY])
             true
@@ -90,8 +91,33 @@ confirm_or_exit() {
     fi
 }
 
-function create_config_file() {
+create_config_file() {
     envsubst < "$1/node.tpl" > "$2"
-    print_step "Config file created at $HOME/.config/vantage6/node/blueberry.yml"
+    print_step "Config file created at $2"
+}
+
+
+check_command() {
+    local command_name="$1"
+
+    # Check if the command is installed
+    if ! command -v "$command_name" &> /dev/null; then
+        print_error "$command_name is not installed" >&2
+        return 1
+    fi
+
+    return 0
+}
+
+check_env() {
+    local env_name="$1"
+
+    # Check if the environment exists
+    if ! conda env list | grep -q "^$env_name "; then
+        print_error "conda environment '$env_name' does not exist" >&2
+        return 1
+    fi
+
+    return 0
 }