no need geoserver test

viewOnTethys2.sh

@@ -0,0 +1,377 @@
+#!/bin/bash
+# ANSI color codes
+BRed='\033[1;31m'
+BGreen='\033[1;32m'
+BYellow='\033[1;33m'
+BBlue='\033[1;34m'
+BPurple='\033[1;35m'
+BCyan='\033[1;36m'
+BWhite='\033[1;37m'
+UBlack='\033[4;30m'
+URed='\033[4;31m'
+UGreen='\033[4;32m'
+UYellow='\033[4;33m'
+UBlue='\033[4;34m'
+UPurple='\033[4;35m'
+UCyan='\033[4;36m'
+UWhite='\033[4;37m'
+
+
+################################################
+###############HELPER FUNCTIONS#################
+################################################
+
+# Function to automatically select file if only one is found
+_auto_select_file() {
+  local files=("$@")  # Correct the handling of arguments as an array
+  if [ "${#files[@]}" -eq 1 ]; then
+    echo "${files[0]}"
+  else
+    echo ""
+  fi
+}
+_check_if_data_folder_exits(){
+    # Check the directory exists
+    if [ ! -d "$DATA_FOLDER_PATH" ]; then
+        echo -e "${BRed}Directory does not exist. Exiting the program.${Color_Off}"
+        exit 0
+    fi
+}
+
+# Check if the config file exists and read from it
+_check_and_read_config() {
+    local config_file="$1"
+    if [ -f "$config_file" ]; then
+        local last_path=$(cat "$config_file")
+        echo -e "Last used data directory path: %s\n" "$last_path"
+        read -erp "Do you want to use the same path? (Y/n): " use_last_path
+        if [[ "$use_last_path" =~ ^[Yy] ]]; then
+            DATA_FOLDER_PATH="$last_path"
+            _check_if_data_folder_exits
+            return 0
+        elif [[ "$use_last_path" =~ ^[Nn] ]]; then
+            read -erp "Enter your input data directory path (use absolute path): " DATA_FOLDER_PATH
+            _check_if_data_folder_exits
+            # Save the new path to the config file
+            echo "$DATA_FOLDER_PATH" > "$CONFIG_FILE"
+            echo -e "The Directory you've given is:\n$DATA_FOLDER_PATH\n"   
+        else
+            echo -e "Invalid input. Exiting.\n" >&2
+            return 1
+        fi
+    fi
+}
+
+_execute_command() {
+  "$@"
+  local status=$?
+  if [ $status -ne 0 ]; then
+    echo -e "${BRed}Error executing command: $1${Color_Off}"
+    _tear_down
+    exit 1
+  fi
+  return $status
+}
+
+_tear_down(){
+    _tear_down_tethys
+    docker network rm $DOCKER_NETWORK > /dev/null 2>&1
+}
+
+_run_containers(){
+    _run_tethys
+}
+
+# Wait for a Docker container to become healthy or unhealthy
+_wait_container() {
+    local container_name=$1
+    local container_health_status
+    local attempt_counter=0
+
+    echo -e "${UPurple}Waiting for container: $container_name to start, this can take a couple of minutes...${Color_Off}\n"
+
+    until [[ "$container_health_status" == "healthy" || "$container_health_status" == "unhealthy" ]]; do
+        # Update the health status
+        if ! container_health_status=$(docker inspect -f '{{.State.Health.Status}}' "$container_name" 2>/dev/null); then
+            echo -e "${BRed}Failed to get health status for container $container_name. Ensure container exists and has a health check.${Color_Off}\n" >&2
+            return 1
+        fi
+
+        if [[ -z "$container_health_status" ]]; then
+            echo -e "${BRed}No health status available for container $container_name. Ensure the container has a health check configured.${Color_Off}\n" >&2
+            return 1
+        fi
+
+        ((attempt_counter++))
+        sleep 2  # Adjusted sleep time to 2 seconds to reduce system load
+    done
+
+    echo -e "${BCyan}Container $container_name is now $container_health_status.${Color_Off}\n"
+    return 0
+}
+
+
+
+_pause_script_execution() {
+    while true; do
+        echo -e "${BYellow}Press q to exit the visualization (default: q/Q):${Color_Off}\n"
+        read -r exit_choice
+
+        if [[ "$exit_choice" =~ ^[qQ]$ ]]; then
+            echo -e "${BRed}Cleaning up Tethys ...${Color_Off}\n"
+            _tear_down
+            exit 0
+        else
+            echo -e "${BRed}Invalid input. Please press 'q' or 'Q' to exit.${Color_Off}\n"
+        fi
+    done
+}
+
+# Function to handle the SIGINT (Ctrl-C)
+handle_sigint() {
+    echo -e "${BRed}Cleaning up . . .${Color_Off}"
+    _tear_down
+    exit 1
+}
+
+check_last_path() {
+    if [[ -z "$1" ]]; then
+        _check_and_read_config "$CONFIG_FILE"
+
+    else
+        DATA_FOLDER_PATH="$1"
+    fi
+    # Finding files
+
+    HYDRO_FABRIC=$(find "$DATA_FOLDER_PATH/config" -iname "*.gpkg")
+    CATCHMENT_FILE=$(find "$DATA_FOLDER_PATH/config" -iname "catchments.geojson")
+    NEXUS_FILE=$(find "$DATA_FOLDER_PATH/config" -iname "nexus.geojson")
+    FLOWPATHTS_FILE=$(find "$DATA_FOLDER_PATH/config" -iname "flowpaths.geojson")
+}
+_get_filename() {
+  local full_path="$1"
+  local filename="${full_path##*/}"
+  echo "$filename"
+}
+
+
+################################################
+###############TETHYS FUNCTIONS#################
+################################################
+
+#create the docker network to communicate between tethys and geoserver
+_create_tethys_docker_network(){
+    _execute_command docker network create -d bridge tethys-network > /dev/null 2>&1
+}
+
+# Link the data to the app workspace
+_link_data_to_app_workspace(){
+    _execute_command docker exec -it $TETHYS_CONTAINER_NAME sh -c \
+        "mkdir -p $APP_WORKSPACE_PATH && \
+        ln -s $TETHYS_PERSIST_PATH/ngen-data $APP_WORKSPACE_PATH/ngen-data"
+}
+
+_convert_gpkg_to_geojson() {
+    local python_bin_path="$1"
+    local path_script="$2"
+    local gpkg_name="$3"
+    local layer_name="$4"
+    local geojson_file="$5"
+    local gpkg_file="$APP_WORKSPACE_PATH/ngen-data/config/$gpkg_name"
+    echo "$gpkg_file"
+    _execute_command docker exec -it \
+        $TETHYS_CONTAINER_NAME \
+        $python_bin_path \
+        $path_script \
+        --convert_to_geojson \
+        --gpkg_path $gpkg_file \
+        --layer_name $layer_name \
+        --output_path $geojson_file
+}
+
+_publish_gpkg_layer_to_geoserver() {
+    local python_bin_path="$1"
+    local path_script="$2"
+    local gpkg_file="$3"
+    local catchment_gpkg_layer="$4"
+    local shapefile_path="$5"
+    local store_name="$6"
+    local geoserver_port="$GEOSERVER_PORT_CONTAINER"
+    local gpkg_file_path="$APP_WORKSPACE_PATH/ngen-data/config/$gpkg_file"
+
+    _execute_command docker exec -it \
+        $TETHYS_CONTAINER_NAME \
+        $python_bin_path \
+        $path_script \
+        --publish \
+        --gpkg_path $gpkg_file_path \
+        --layer_name $catchment_gpkg_layer \
+        --shp_path "$shapefile_path" \
+        --store_name $store_name \
+        --geoserver_host $GEOSERVER_CONTAINER_NAME \
+        --geoserver_port $geoserver_port \
+        --geoserver_username $GEOSERVER_ADMIN_USER \
+        --geoserver_password $GEOSERVER_ADMIN_PASSWORD
+}
+
+_publish_geojson_layer_to_geoserver() {
+    local python_bin_path="$1"
+    local path_script="$2"
+    local geojson_path="$3"
+    local shapefile_path="$4"
+    local store_name="$5"
+    _execute_command docker exec -it \
+        $TETHYS_CONTAINER_NAME \
+        $python_bin_path \
+        $path_script \
+        --publish_geojson \
+        --geojson_path $geojson_path \
+        --shp_path "$shapefile_path" \
+        --store_name $store_name \
+        --geoserver_host $GEOSERVER_CONTAINER_NAME \
+        --geoserver_port $GEOSERVER_PORT_CONTAINER \
+        --geoserver_username $GEOSERVER_ADMIN_USER \
+        --geoserver_password $GEOSERVER_ADMIN_PASSWORD
+}
+
+_create_geoserver_workspace() {
+    local python_bin_path="$1"
+    local path_script="$2"
+    _execute_command docker exec -it \
+        $TETHYS_CONTAINER_NAME \
+        $python_bin_path \
+        $path_script \
+        --create_workspace \
+        --geoserver_host $GEOSERVER_CONTAINER_NAME \
+        --geoserver_port $GEOSERVER_PORT_CONTAINER \
+        --geoserver_username $GEOSERVER_ADMIN_USER \
+        --geoserver_password $GEOSERVER_ADMIN_PASSWORD
+}
+
+
+
+_check_for_existing_tethys_image() {
+    echo -e "${BYellow}Select an option (type a number): ${Color_Off}\n"
+    options=("Run Tethys using existing local docker image" "Run Tethys after updating to latest docker image" "Exit")
+    select option in "${options[@]}"; do
+        case $option in
+            "Run Tethys using existing local docker image")
+                echo -e "${BGreen}Using local image of the Tethys platform${Color_Off}\n"
+                return 0
+                ;;
+            "Run Tethys after updating to latest docker image")
+                echo -e "${BGreen}Pulling container...${Color_Off}\n"
+                if ! docker pull "$TETHYS_IMAGE_NAME"; then
+                    echo -e "${BRed}Failed to pull Docker image: $TETHYS_IMAGE_NAME${Color_Off}\n" >&2
+                    return 1
+                fi
+                return 0
+                ;;
+            "Exit")
+                echo -e "${BCyan}Have a nice day!${Color_Off}\n"
+                _tear_down
+                exit 0
+                ;;
+            *)
+                echo -e "${BRed}Invalid option $REPLY, 1 to continue with existing local image, 2 to update and run, and 3 to exit${Color_Off}\n"
+                ;;
+        esac
+    done
+}
+
+
+_tear_down_tethys(){
+    if [ "$(docker ps -aq -f name=$TETHYS_CONTAINER_NAME)" ]; then
+        docker stop $TETHYS_CONTAINER_NAME > /dev/null 2>&1
+    fi
+}
+
+
+_run_tethys(){
+    _execute_command docker run --rm -it -d \
+    -v "$DATA_FOLDER_PATH:$TETHYS_PERSIST_PATH/ngen-data" \
+    -p 80:80 \
+    --platform $PLATFORM \
+    --network $DOCKER_NETWORK \
+    --name "$TETHYS_CONTAINER_NAME" \
+    --env MEDIA_ROOT="$TETHYS_PERSIST_PATH/media" \
+    --env MEDIA_URL="/media/" \
+    --env SKIP_DB_SETUP=$SKIP_DB_SETUP \
+    $TETHYS_IMAGE_NAME \
+    > /dev/null 2>&1
+}
+
+
+# Create tethys portal
+create_tethys_portal(){
+    while true; do
+        echo -e "${BYellow}Visualize outputs using the Tethys Platform (https://www.tethysplatform.org/)? (y/N, default: y):${Color_Off}"
+        read -r visualization_choice
+
+        # Default to 'y' if input is empty
+        if [[ -z "$visualization_choice" ]]; then
+            visualization_choice="y"
+        fi
+
+        # Check for valid input
+        if [[ "$visualization_choice" == [YyNn]* ]]; then
+            break
+        else
+            echo -e "${BRed}Invalid choice. Please enter 'y' for yes, 'n' for no, or press Enter for default (yes).${Color_Off}"
+        fi
+    done
+
+    # Execute the command
+    if [[ "$visualization_choice" == [Yy]* ]]; then
+        echo -e "${BGreen}Setup Tethys Portal image...${Color_Off}"
+        _create_tethys_docker_network
+        if _check_for_existing_tethys_image; then
+            _execute_command _run_containers
+            echo -e "${BCyan}Link data to the Tethys app workspace.${Color_Off}"
+            _link_data_to_app_workspace
+            _wait_container $TETHYS_CONTAINER_NAME
+            echo -e "${BGreen}Your outputs are ready to be visualized at http://localhost/apps/ngiab ${Color_Off}"
+            echo -e "${UPurple}You can use the following to login: ${Color_Off}"
+            echo -e "${BCyan}user: admin${Color_Off}"
+            echo -e "${BCyan}password: pass${Color_Off}"
+            echo -e "${UPurple}Check the App source code: https://github.com/Aquaveo/ngiab-client ${Color_Off}"
+            _pause_script_execution
+        else
+            echo -e "${BRed}Failed to prepare Tethys portal.${Color_Off}\n"
+        fi
+    else
+        echo -e "${BCyan}Skipping Tethys visualization setup.${Color_Off}\n"
+    fi
+}
+
+
+##########################
+#####START OF SCRIPT######
+##########################
+
+# Set up the SIGINT trap to call the handle_sigint function
+trap handle_sigint SIGINT
+
+# Constanst
+PLATFORM='linux/amd64'
+TETHYS_CONTAINER_NAME="tethys-ngen-portal"
+DOCKER_NETWORK="tethys-network"
+APP_WORKSPACE_PATH="/usr/lib/tethys/apps/ngiab/tethysapp/ngiab/workspaces/app_workspace"
+TETHYS_IMAGE_NAME=awiciroh/tethys-ngiab:main
+DATA_FOLDER_PATH="$1"
+TETHYS_PERSIST_PATH="/var/lib/tethys_persist"
+CONFIG_FILE="$HOME/.host_data_path.conf"
+SKIP_DB_SETUP=false
+
+# check for architecture
+if uname -a | grep arm64 || uname -a | grep aarch64 ; then
+    PLATFORM=linux/arm64
+else
+    PLATFORM=linux/amd64
+fi
+
+
+check_last_path "$@"
+
+create_tethys_portal
+