Modified scripts for IDEA4RC project

create-cronjob.sh

@@ -8,7 +8,7 @@ source $SCRIPT_DIR/utils.sh
 print_step "Adding cron job"
 if ! check_command "crontab"; then
     print_warning "Crontab not installed. Installing crontab."
-    sudo dnf install crontabs -y &>> $LOG_DIR/install-crontab.log
+    sudo apt install cron -y &>> $LOG_DIR/install-crontab.log
 fi
 if ! (crontab -l 2>/dev/null | grep -q "$SCRIPT_DIR/start.sh"); then
     (crontab -l 2>/dev/null; echo "@reboot $SCRIPT_DIR/start.sh") | crontab -

create-node.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 source $SCRIPT_DIR/utils.sh
-CONFIG_FILE=$HOME/.config/vantage6/node/blueberry.yaml
+CONFIG_FILE=$HOME/.config/vantage6/node/idea4rc.yaml
 CONFIG_FILE_TEMPLATE=$SCRIPT_DIR/node.tpl
 
 WRITE_CONFIG_FILE=true
@@ -55,62 +55,42 @@ if [ "$WRITE_CONFIG_FILE" = true ]; then
     export API_KEY=$API_KEY
 
     # OMOP database settings
-    if is_set "OMOP_HOST" "silent"; then
-        if is_set "DOCKER_SERVICE_CONTAINER_LABEL" "silent"; then
-            print_step "Using previous Docker service container label: $DOCKER_SERVICE_CONTAINER_LABEL"
-            DB_METHOD="Docker-service"
-        else
-            print_step "Using previous SSH OMOP_HOST: $OMOP_HOST"
-            DB_METHOD="SSH-tunnel"
-        fi
-    else
-        # depending on the method selected we need to inject a different block in the
-        # config file
-        select_database_method
-    fi
+    is_set_or_prompt "OMOP_API_PROTOCOL" "http/https"
+    export OMOP_API_PROTOCOL=$OMOP_API_PROTOCOL
+    is_set_or_prompt "OMOP_API_URI" "ip or domain"
+    export OMOP_API_URI=$OMOP_API_URI
+    is_set_or_prompt "OMOP_API_PORT" "typically 80 or 443"
+    export OMOP_API_PORT=$OMOP_API_PORT
+
+    select_whitelist_method
 
-    is_set_or_prompt "OMOP_PORT"
-    export OMOP_PORT=$OMOP_PORT
-    is_set_or_prompt "OMOP_DATABASE"
-    export OMOP_DATABASE=$OMOP_DATABASE
-    is_set_or_prompt "OMOP_USER"
-    export OMOP_USER=$OMOP_USER
-    is_set_or_prompt "OMOP_PASSWORD"
-    export OMOP_PASSWORD=$OMOP_PASSWORD
-    is_set_or_prompt "OMOP_CDM_SCHEMA"
-    export OMOP_CDM_SCHEMA=$OMOP_CDM_SCHEMA
-    is_set_or_prompt "OMOP_RESULT_SCHEMA"
-    export OMOP_RESULT_SCHEMA=$OMOP_RESULT_SCHEMA
-
-    case "$DB_METHOD" in
-        "Docker-service")
+    case "$WHITELIST_VERSION" in
+        "Domain")
             # Code to execute if DB_METHOD is "docker"
-            if ! is_set "OMOP_HOST" "silent"; then
-                user_input "Please enter the OMOP container name"
-                OMOP_HOST=$REPLY
-            fi
 
-            export OMOP_HOST=$OMOP_HOST
-            export DOCKER_SERVICE_CONTAINER_LABEL=$OMOP_HOST
-            include_content=$(<$SCRIPT_DIR/templates/docker-service.tpl)
+            is_set_or_prompt "WHITELIST_DOMAIN"
+            export WHITELIST_DOMAIN=$WHITELIST_DOMAIN
+            include_content=$(<$SCRIPT_DIR/templates/whitelist-domain.tpl)
 
             ;;
-        "SSH-tunnel")
+        "IP")
             # Code to execute if DB_METHOD is "ssh_tunnel"
-            export OMOP_HOST="omop"
-            include_content=$(<$SCRIPT_DIR/templates/ssh-tunnel.tpl)
-            source $SCRIPT_DIR/create-ssh-tunnel.sh
+            is_set_or_prompt "WHITELIST_IP"
+            export WHITELIST_IP=$WHITELIST_IP
+            include_content=$(<$SCRIPT_DIR/templates/whitelist-ip.tpl)
             ;;
         *)
             # Code to execute if DB_METHOD is anything else
-            print_error "Invalid option $DB_METHOD. Exiting..."
+            print_error "Invalid option $WHITELIST_VERSION. Exiting..."
             exit 1
             ;;
     esac
+    is_set_or_prompt "WHITELIST_PORT"
+    export WHITELIST_PORT=$WHITELIST_PORT
 
     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 > $CONFIG_FILE_TEMPLATE
+    sed "s/{{WHITELIST}}/$escaped_content/g" $SCRIPT_DIR/templates/node-config.tpl | sed 's/NEWLINE/\n/g' > $CONFIG_FILE_TEMPLATE
+    # sed "s/{{WHITELIST}}/$escaped_content/" $SCRIPT_DIR/templates/node-config.tpl > $CONFIG_FILE_TEMPLATE
 
     # # Create the config file
     print_step "Creating the config file"
@@ -122,17 +102,20 @@ if [ "$WRITE_CONFIG_FILE" = true ]; then
     if [ "$KEEP_PREVIOUS_SETTINGS" = false ]; then
         print_step "Creating environment file"
         echo "export API_KEY=$API_KEY" > $SCRIPT_DIR/settings.env
-        echo "export OMOP_PORT=$OMOP_PORT" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_DATABASE=$OMOP_DATABASE" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_USER=$OMOP_USER" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_PASSWORD=$OMOP_PASSWORD" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_CDM_SCHEMA=$OMOP_CDM_SCHEMA" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_RESULT_SCHEMA=$OMOP_RESULT_SCHEMA" >> $SCRIPT_DIR/settings.env
-        echo "export OMOP_HOST=$OMOP_HOST" >> $SCRIPT_DIR/settings.env
-        if is_set "DOCKER_SERVICE_CONTAINER_LABEL" "silent"; then
-            echo "export DOCKER_SERVICE_CONTAINER_LABEL=$DOCKER_SERVICE_CONTAINER_LABEL" >> $SCRIPT_DIR/settings.env
+
+        echo "export OMOP_API_PROTOCOL=$OMOP_API_PROTOCOL" >> $SCRIPT_DIR/settings.env
+        echo "export OMOP_API_URI=$OMOP_API_URI" >> $SCRIPT_DIR/settings.env
+        echo "export OMOP_API_PORT=$OMOP_API_PORT" >> $SCRIPT_DIR/settings.env
+
+        if is_set "WHITELIST_DOMAIN" "silent"; then
+            echo "export WHITELIST_DOMAIN=$WHITELIST_DOMAIN" >> $SCRIPT_DIR/settings.env
         fi
+        if is_set "WHITELIST_IP" "silent"; then
+            echo "export WHITELIST_IP=$WHITELIST_IP" >> $SCRIPT_DIR/settings.env
+        fi
+        echo "export WHITELIST_PORT=$WHITELIST_PORT" >> $SCRIPT_DIR/settings.env
     fi
+
 fi
 
 

install-all.sh

@@ -11,13 +11,10 @@ mkdir -p $LOG_DIR
 
 # Update the current system
 print_header "Updating the current system (this may take a while)"
-sudo dnf update -y &>> $LOG_DIR/update-system.log
+sudo apt update &>> $LOG_DIR/update-system.log
+sudo apt upgrade -y &>> $LOG_DIR/update-system.log
 print_step "System updated"
 
-# Run the install-docker.sh script
-print_header "Installing Docker"
-source $SCRIPT_DIR/install-docker.sh
-
 # Run the install-miniconda.sh script
 print_header "Installing Miniconda"
 source $SCRIPT_DIR/install-miniconda.sh

install-miniconda.sh

@@ -9,6 +9,13 @@ print_step "Checking if Miniconda is already installed"
 if command -v conda &> /dev/null; then
     print_warning "Miniconda is already installed." | tee -a $LOG_DIR/miniconda-install.log
 else
+
+    print_step "Check that curl is installed"
+    if ! check_command "curl"; then
+        print_warning "Curl not installed. Installing Curl"
+        sudo apt install curl -y &>> $LOG_DIR/miniconda-install.log
+    fi
+
     # 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 &>> $LOG_DIR/miniconda-install.log

templates/node-config.tpl

@@ -51,23 +51,24 @@ databases:
   #   uri: C:\data\datafile.csv
   #   type: csv
 
-  - label: omop
-    uri: jdbc:postgresql://${OMOP_HOST}:${OMOP_PORT}/${OMOP_DATABASE}
-    type: omop
+  - label: omop_api
+    uri: ${OMOP_API_PROTOCOL}://${OMOP_API_URI}:${OMOP_API_PORT}
+    type: other
     # 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
     # only passed to the algorithm container when the user requests that
     # database. In case you want to pass some environment variable to all
     # algorithms regard less of the data source the user specifies you can
     # use the `algorithm_env` setting.
-    env:
-      user: ${OMOP_USER}
-      password: ${OMOP_PASSWORD}
-      dbms: postgresql
-      cdm_database: ${OMOP_DATABASE}
-      cdm_schema: ${OMOP_CDM_SCHEMA}
-      results_schema: ${OMOP_RESULT_SCHEMA}
+    # env:
+    #   user: ${OMOP_USER}
+    #   password: ${OMOP_PASSWORD}
+    #   dbms: postgresql
+    #   cdm_database: ${OMOP_DATABASE}
+    #   cdm_schema: ${OMOP_CDM_SCHEMA}
+    #   results_schema: ${OMOP_RESULT_SCHEMA}
+
 
 
 # end-to-end encryption settings
@@ -108,7 +109,7 @@ policies:
 #     username: docker-registry-user
 #     password: docker-registry-password
 
-{{DATABASE_CONNECTION}}
+{{WHITELIST}}
 
 # # Whitelist URLs and/or IP addresses that the algorithm containers are
 # # allowed to reach using the http protocol.