Added option to use docker container over ssh tunnel

.gitignore

@@ -1,2 +1,3 @@
 
 *.log
+/node.tpl

README.md

@@ -2,24 +2,22 @@
 
 This repository contains convenience scripts for installing vantage6 nodes at data stations participating in the BLUEBERRY project.
 
-## TODO
-- [ ] Add option to use Docker version of the OMOP database (no SSH tunneling required)
-
 ## Getting Started
 These instructions will get you a running vantage6 node that is connected to the
 BLUEBERRY server.
 
 ### Prerequisites
 
-The scripts are designed to run on an Oracle Linux 8 Machine (server edition). During installation it requires internet access to download the necessary packages.
+- The scripts are designed to run on an Oracle Linux 8 Machine (server edition).
+- During installation it requires internet access to download the necessary packages.
+- `sudo` permissions
+- Install git:
+    ```
+    sudo dnf update -y
+    sudo dnf install git -y
+    ```
 
-Install git:
-```
-sudo dnf update -y
-sudo dnf install git -y
-```
 
-It also requires an active internet connection.
 
 ### Installing
 

create-node.sh

@@ -1,6 +1,7 @@
 #! /bin/bash
 source $SCRIPT_DIR/utils.sh
 CONFIG_FILE=$HOME/.config/vantage6/node/blueberry.yaml
+CONFIG_FILE_TEMPLATE=$SCRIPT_DIR/node.tpl
 
 WRITE_CONFIG_FILE=true
 if [ -f "$CONFIG_FILE" ]; then
@@ -13,6 +14,7 @@ if [ -f "$CONFIG_FILE" ]; then
     fi
 fi
 
+
 if [ "$WRITE_CONFIG_FILE" = true ]; then
 
     # Create config dir
@@ -29,66 +31,50 @@ if [ "$WRITE_CONFIG_FILE" = true ]; then
 
     mkdir -p $TASK_DIR
 
-    # OMOP settings
-    export OMOP_HOST="omop"
+    # OMOP database settings
     export OMOP_PORT=5432
-
     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_warning "The vantage6-node user already exists"
-    else
-        print_step "Creating new user: $NEW_USER"
-        sudo useradd $NEW_USER
-
-        # Set password for the new user
-        PASSWORD=$(openssl rand -base64 16)
-        echo "$NEW_USER:$PASSWORD" | sudo chpasswd
-    fi
-
-
-    print_step "Executing some steps as sudo user"
-    source $SCRIPT_DIR/create-ssh-user.sh
-
-    # Tunnel settings
-    print_step "Setting tunnel settings"
-    export TUNNEL_HOSTNAME=$OMOP_HOST
-    export SSH_HOST=$(ip addr show eth0 | grep 'inet ' | awk '{print $2}' | cut -d/ -f1)
-    export SSH_PORT=22
-    print_step "SSH_HOST: $SSH_HOST, SSH_PORT: $SSH_PORT"
-
-
-    if [ -f "/etc/ssh/ssh_host_rsa_key.pub" ]; then
-        export SSH_HOST_FINGERPRINT=$(cat /etc/ssh/ssh_host_rsa_key.pub)
-    else
-        print_error "File /etc/ssh/ssh_host_rsa_key.pub does not exist."
-        print_error "Is openssh-server installed and running?"
-    fi
-
-    export SSH_USERNAME=$NEW_USER
-    export SSH_KEY=$PRIVATE_KEY_FILE
-    print_step "SSH_KEY: $SSH_KEY"
-
-    export TUNNEL_BIND_IP="0.0.0.0"
-    export TUNNEL_BIND_PORT=$OMOP_PORT
-
-    export TUNNEL_REMOTE_IP="127.0.0.1"
-    export TUNNEL_REMOTE_PORT=5432
-    print_step "TUNNEL_REMOTE_PORT: $TUNNEL_REMOTE_PORT"
+    # depending on the method selected we need to inject a different block in the
+    # config file
+    select_database_method
+
+    case "$DB_METHOD" in
+        "Docker-service")
+            # Code to execute if DB_METHOD is "docker"
+            user_input "Please enter the OMOP container name"
+            export OMOP_HOST=$REPLY
+            export DOCKER_SERVICE_CONTAINER_LABEL=$REPLY
+            include_content=$(<$SCRIPT_DIR/templates/docker-service.tpl)
+
+            ;;
+        "SSH-tunnel")
+            # Code to execute if DB_METHOD is "ssh_tunnel"
+            export OMOP_HOST="omop"
+            include_content=$(<$SCRIPT_DIR/templates/ssh-tunnel.tpl)
+            source $SCRIPT_DIR/create-ssh-tunnel.sh
+            ;;
+        *)
+            # Code to execute if DB_METHOD is anything else
+            print_error "Invalid option $DB_METHOD. Exiting..."
+            exit 1
+            ;;
+    esac
+
+    escaped_content=$(echo "$include_content" | sed -e ':a' -e 'N' -e '$!ba' -e 's/[\/&]/\\&/g' -e 's/\n/NEWLINE/g')
+    sed "s/{{DATABASE_CONNECTION}}/$escaped_content/g" $SCRIPT_DIR/templates/node-config.tpl | sed 's/NEWLINE/\n/g' > $CONFIG_FILE_TEMPLATE
+    # sed "s/{{DATABASE_CONNECTION}}/$escaped_content/" $SCRIPT_DIR/templates/node-config.tpl > $CONFIG_FILE_TEMPLATE
 
     # # Create the config file
     print_step "Creating the config file"
     mkdir -p $HOME/.config/vantage6/node
 
     print_step "Creating the vantage6 config file"
-    create_config_file $SCRIPT_DIR $CONFIG_FILE
+    create_config_file $CONFIG_FILE_TEMPLATE $CONFIG_FILE
 fi
 
 

create-ssh-tunnel.sh

@@ -0,0 +1,47 @@
+
+    #! /bin/bash
+    source $SCRIPT_DIR/utils.sh
+
+    # 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_warning "The vantage6-node user already exists"
+    else
+        print_step "Creating new user: $NEW_USER"
+        sudo useradd $NEW_USER
+
+        # Set password for the new user
+        PASSWORD=$(openssl rand -base64 16)
+        echo "$NEW_USER:$PASSWORD" | sudo chpasswd
+    fi
+
+
+    print_step "Executing some steps as sudo user"
+    source $SCRIPT_DIR/create-ssh-keys.sh
+
+    # Tunnel settings
+    print_step "Setting tunnel settings"
+    export TUNNEL_HOSTNAME=$OMOP_HOST
+    export SSH_HOST=$(ip addr show eth0 | grep 'inet ' | awk '{print $2}' | cut -d/ -f1)
+    export SSH_PORT=22
+    print_step "SSH_HOST: $SSH_HOST, SSH_PORT: $SSH_PORT"
+
+
+    if [ -f "/etc/ssh/ssh_host_rsa_key.pub" ]; then
+        export SSH_HOST_FINGERPRINT=$(cat /etc/ssh/ssh_host_rsa_key.pub)
+    else
+        print_error "File /etc/ssh/ssh_host_rsa_key.pub does not exist."
+        print_error "Is openssh-server installed and running?"
+    fi
+
+    export SSH_USERNAME=$NEW_USER
+    export SSH_KEY=$PRIVATE_KEY_FILE
+    print_step "SSH_KEY: $SSH_KEY"
+
+    export TUNNEL_BIND_IP="0.0.0.0"
+    export TUNNEL_BIND_PORT=$OMOP_PORT
+
+    export TUNNEL_REMOTE_IP="127.0.0.1"
+    export TUNNEL_REMOTE_PORT=5432
+    print_step "TUNNEL_REMOTE_PORT: $TUNNEL_REMOTE_PORT"

templates/docker-service.tpl

@@ -0,0 +1,2 @@
+docker_services:
+    container_label: ${DOCKER_SERVICE_CONTAINER_LABEL}