#! /bin/sh -e

# genenetwork-machines --- Guix configuration for genenetwork machines
# Copyright © 2025 Munyoki Kilyungi <me@bonfacemunyoki.com>
#
# This file is part of genenetwork-machines.
#
# genenetwork-machines is free software: you can redistribute it
# and/or modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# genenetwork-machines is distributed in the hope that it will be
# useful, but WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with genenetwork-machines.  If not, see
# <https://www.gnu.org/licenses/>.

# Build and install genenetwork container on your local machine.

set -euo pipefail


BASE_DIR="${HOME:-/home/$USER}/genenetwork"
SYSTEM_DIRECTORIES=(
    "$BASE_DIR"
    "$BASE_DIR/var/log"
    "$BASE_DIR/var/genenetwork"
    "$BASE_DIR/etc/genenetwork/conf"
    "$BASE_DIR/etc/genenetwork"
    "$BASE_DIR/var/lib/redis"
    "$BASE_DIR/var/lib/virtuoso"
    "$BASE_DIR/var/lib/data"
    "$BASE_DIR/var/lib/gn-uploader/data"
    "$BASE_DIR/var/lib/gn-uploader/sessions"
    "$BASE_DIR/var/lib/xapian"
    "$BASE_DIR/var/genenetwork/genotype-files/genotype/json"
    "$BASE_DIR/var/lib/genenetwork-sqlite"
    "$BASE_DIR/var/lib/genenetwork-gnqa"
    "/tmp/local-container"
)

GN_PROJECTS=(
    "genenetwork2:https://github.com/genenetwork/genenetwork2.git"
    "genenetwork3:https://github.com/genenetwork/genenetwork3.git"
    "gn-transform-databases:https://git.genenetwork.org/gn-transform-databases/"
    "gn-auth:https://git.genenetwork.org/gn-auth"
    "gn-docs:https://git.genenetwork.org/gn-docs"
    "gn-uploader:https://git.genenetwork.org/gn-uploader"
)

# File mappings: source -> destination
declare -A FILE_MAPPINGS=(
    ["etc/auth.db"]="$BASE_DIR/var/genenetwork/auth.db"
    ["etc/gn-uploader.db"]="$BASE_DIR/var/genenetwork/gn-uploader.db"
    ["etc/llm.db"]="$BASE_DIR/var/lib/genenetwork-sqlite/llm.db"
    ["etc/gn2-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn2/secrets.py"
    ["etc/gn3-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn3/secrets.py"
    ["etc/gn-auth-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn-auth/secrets.py"
    ["etc/gn-uploader-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn-uploader/secrets.py"
)

CONTAINER_SCM="genenetwork-local-container.scm"
CONTAINER_BIN="/usr/local/bin/genenetwork-local-container"
GC_ROOT="/var/guix/gcroots/genenetwork-local-container"

log() {
    local level="$1"
    shift
    echo "[$(date '+%Y-%m-%d %H:%M:%S')] $level: $*" >&2
}

# Check dependencies
for cmd in git sudo diff cp grep; do
    if ! command -v "$cmd" &>/dev/null; then
        log "ERROR" "Required command '$cmd' not found"
        exit 1
    fi
done

if ! command -v guix &>/dev/null; then
    echo "Please install Guix to proceed. Follow the instructions at:"
    echo "https://issues.genenetwork.org/topics/octopus/set-up-guix-for-new-users"
    echo "After installing Guix, try running this script again."
    exit 1
fi

# Check for gn-bioinformatics channel
guix describe | grep gn-bioinformatics\
    &> /dev/null && log "INFO" "guix guix-informatics $(guix describe | grep gn-bioinformatics | cut -d ' ' -f 4)" || \
	(clear && guix describe &&
	     echo ""
	     log "ERROR" "Please make sure your current profile has gn-bioinformatics" &&
	     echo "" &&
	     echo "Refer to:" &&
	     echo "    https://issues.genenetwork.org/topics/guix/guix-profiles" &&
	     echo "to help you set your profile" && echo "" &&
	     exit 1)

# Validate HOME is set
if [ -z "${HOME:-}" ]; then
    log "ERROR" "HOME environment variable is not set"
    exit 1
fi

init_container() {
    log "INFO" "Creating system directories..."
    for dir in "${SYSTEM_DIRECTORIES[@]}"; do
	# Check if directory exists and is accessible
	if [ -d "$dir" ]; then
            if [ -w "$dir" ]; then
		log "DEBUG" "Directory exists and is writable: $dir"
            else
		log "WARNING" "Directory exists but is not writable: $dir.  Making this writable"
		sudo chown -R "$USER" "$dir"
            fi
            continue
	fi

	# Attempt to create directory
	log "INFO" "Creating directory: $dir"
	if [ -w "$(dirname "$dir")" ]; then
            # Parent directory is writable, try without sudo
            if ! mkdir -p "$dir"; then
		log "ERROR" "Failed to create directory without sudo: $dir"
		exit 1
            fi
	else
            # Parent directory requires root, use sudo
            if ! sudo mkdir -p "$dir"; then
		log "ERROR" "Failed to create directory with sudo: $dir"
		exit 1
            fi
            # Set ownership to current user if created with sudo
            if ! sudo chown -R "$USER" "$dir"; then
		log "WARNING" "Failed to set ownership for: $dir"
            fi
	fi
    done

    # Check and copy configuration files
    log "INFO" "Checking and copying configuration files..."
    for src in "${!FILE_MAPPINGS[@]}"; do
	dest="${FILE_MAPPINGS[$src]}"
	log "INFO" "Processing $src -> $dest"

	# Check if source file exists
	if [ ! -f "$src" ]; then
            log "ERROR" "Source file does not exist: $src"
            exit 1
	fi

	# Check if destination file exists
	if [ ! -f "$dest" ]; then
            log "INFO" "Destination file does not exist, copying $src to $dest"
            mkdir -p "$(dirname "$dest")"
            if ! cp "$src" "$dest"; then
		log "ERROR" "Failed to copy $src to $dest"
		exit 1
            fi
            continue
	fi

	# Compare files using diff
	log "INFO" "Comparing $src with $dest"
	if diff_output=$(diff -u "$dest" "$src" 2>&1); then
            log "INFO" "Files $src and $dest are identical"
	else
            log "INFO" "Differences found between $src and $dest:"
            echo "$diff_output" >&2
            log "INFO" "Copying $src to $dest"
            if ! cp "$src" "$dest"; then
		log "ERROR" "Failed to copy $src to $dest"
		exit 1
            fi
	fi
    done

    is_git_repository() {
	local dir="$1"
	# Check for standard repository
	if [ -d "$dir/.git" ]; then
            if [ -f "$dir/.git/HEAD" ] && [ -d "$dir/.git/refs" ]; then
		log "DEBUG" "Detected standard Git repository: $dir"
		return 0
            else
		log "ERROR" "Directory $dir/.git exists but is not a valid Git repository"
		return 1
            fi
	    # Check for bare repository
	elif [ -f "$dir/HEAD" ] && [ -d "$dir/refs" ] && [ -d "$dir/objects" ]; then
            log "DEBUG" "Detected bare Git repository: $dir"
            return 0
	else
            log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)"
            return 1
	fi
    }
    # Clone GeneNetwork projects
    log "INFO" "Cloning GeneNetwork projects..."
    for project_entry in "${GN_PROJECTS[@]}"; do
	IFS=':' read -r project repo_url <<< "$project_entry"
	dir="$BASE_DIR/$project"
	if [ ! -d "$dir" ]; then
            log "INFO" "Cloning $project from $repo_url to $dir"
            if ! git clone "$repo_url" "$dir"; then
		log "ERROR" "Failed to clone $project"
		exit 1
            fi
	else
            log "DEBUG" "Directory exists, skipping clone: $dir"
            if ! is_git_repository "$dir"; then
		log "ERROR" "$dir exists but is not a Git repository"
		exit 1
            fi
	fi
    done

    FLASK_SESSIONS=(
	"gn-uploader:$BASE_DIR/gn-uploader/flask_session"
	"genenetwork2:$BASE_DIR/genenetwork2/flask_session"
    )
    for flask_session in "${FLASK_SESSIONS[@]}"; do
	IFS=':' read -r project session_dir <<< "$flask_session"
	if [ ! -d "$session_dir" ]; then
	    log "INFO" "Creating FLASK_SESSION directory: $session_dir"
	    if ! mkdir -p "$session_dir"; then
		log "ERROR" "Failed to create FLASK_SESSION directory: $session_dir"
		exit 1
	    fi
	else
	    log "DEBUG" "FLASK_SESSION directory already exists: $session_dir"
	fi
    done

    # Verify container SCM file exists
    if [ ! -f "$CONTAINER_SCM" ]; then
	log "ERROR" "Container SCM file not found: $CONTAINER_SCM"
	exit 1
    fi

    # Create Guix system container
    log "INFO" "Creating Guix system container..."
    SHARE_OPTS=(
	"--share=$BASE_DIR/var/log=/var/log"
	"--share=$BASE_DIR/var/genenetwork=/var/genenetwork"
	"--share=$BASE_DIR/etc/genenetwork/conf=/etc/genenetwork/conf"
	"--share=$BASE_DIR/etc/genenetwork=/etc/genenetwork"
	"--share=$BASE_DIR/var/lib/redis=/var/lib/redis"
	"--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso"
	"--share=$BASE_DIR/var/lib/data=/var/lib/data"
	"--share=$BASE_DIR/var/lib/gn-uploader/data=/var/lib/gn-uploader/data"
	"--share=$BASE_DIR/var/lib/gn-uploader/sessions=/var/lib/gn-uploader/sessions"
	"--share=$BASE_DIR/genenetwork2=/genenetwork2"
	"--share=$BASE_DIR/genenetwork3=/genenetwork3"
	"--share=$BASE_DIR/gn-uploader=/gn-uploader"
	"--share=$BASE_DIR/gn-auth=/gn-auth"
	"--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian"
	"--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite"
	"--share=$BASE_DIR/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa"
	"--share=/tmp/local-container=/tmp"
	"--share=$BASE_DIR/gn-docs=/var/lib/gn-docs"
	"--share=/run/mysqld=/run/mysqld"
    )

    container_script=$(guix system container \
			    --network --fallback \
			    --load-path=. \
			    --verbosity=3 \
			    "${SHARE_OPTS[@]}" \
			    "$CONTAINER_SCM")

    log $container_script

    # Create symbolic links
    log "INFO" "Creating symbolic links..."
    if ! sudo ln -sf "$container_script" "$CONTAINER_BIN"; then
	log "ERROR" "Failed to create symbolic link: $CONTAINER_BIN"
	exit 1
    fi

    if ! sudo ln -sf "$container_script" "$GC_ROOT"; then
	log "ERROR" "Failed to create GC root link: $GC_ROOT"
	exit 1
    fi

    log "INFO" "Setup completed successfully!"
    log "INFO" "Container script: $container_script"
    log "INFO" "Run with: $CONTAINER_BIN"
    log "INFO" "Email: test@development.user"
    log "INFO" "Password: testpasswd"
}

if [ "$1" = "--init-container" ]; then
    init_container
    exit 0
fi

init_sql() {
    # Configuration
    URL="https://files.genenetwork.org/database/db_webqtl_s-2025-02-18.sql.xz"
    DOWNLOAD_DIR="/tmp"
    FILE_NAME=$(basename "$URL")
    EXTRACTED_FILE="${FILE_NAME%.xz}"
    DB_USER="webqtlout"
    DB_PASSWORD="webqtlout"
    DB_HOST="localhost"
    DB_NAME="db_webqtl_local"
    MYSQL_ROOT_USER=""  # Change to your MySQL admin user if different
    MYSQL_ROOT_PASSWORD=""   # Set this or leave empty to prompt

    # Check for required tools
    for cmd in wget xz mysql; do
	if ! command -v "$cmd" &> /dev/null; then
            log ERROR "Required command '$cmd' not found"
            exit 1
	fi
    done

    # Extract the .xz file
    if [ ! -f "/tmp/db_webqtl_s-2025-02-18.sql" ]; then
       # Download the file
       log INFO "Downloading $URL to $DOWNLOAD_DIR/$FILE_NAME"
       if ! wget -O "$DOWNLOAD_DIR/$FILE_NAME" "$URL"; then
	   log ERROR "Failed to download $URL"
	   exit 1
       fi

       log INFO "Extracting $DOWNLOAD_DIR/$FILE_NAME"
       if ! xz -d "$DOWNLOAD_DIR/$FILE_NAME"; then
	   log ERROR "Failed to extract $DOWNLOAD_DIR/$FILE_NAME"
	   rm -f "$DOWNLOAD_DIR/$FILE_NAME"
	   exit 1
       fi
    fi

    # Prepare MySQL user and password credentials
    if [ -z "$MYSQL_ROOT_USER" ]; then
	log INFO "MySQL root user not set, prompting for input"
	read -s -p "Enter MySQL user: " MYSQL_ROOT_USER
    fi
    if [ -z "$MYSQL_ROOT_PASSWORD" ]; then
	log INFO "MySQL root password not set, prompting for input"
	read -s -p "Enter MySQL root password: " MYSQL_ROOT_PASSWORD
    fi

    # Check if DB user exists, create if not
    log INFO "Checking if MySQL user $DB_USER exists"
    USER_EXISTS=$(mysql -h "$DB_HOST" -u "$MYSQL_ROOT_USER" -p"$MYSQL_ROOT_PASSWORD" -e "SELECT EXISTS(SELECT 1 FROM mysql.user WHERE user = '$DB_USER' AND host = 'localhost') AS user_exists;" 2>/dev/null | grep -o '[0-1]$')
    if [ "$USER_EXISTS" = "0" ]; then
	log INFO "Creating MySQL user $DB_USER"
	if ! mysql -h "$DB_HOST" -u "$MYSQL_ROOT_USER" -p"$MYSQL_ROOT_PASSWORD" -e "CREATE USER '$DB_USER'@'localhost' IDENTIFIED BY '$DB_PASSWORD'; GRANT ALL PRIVILEGES ON $DB_NAME.* TO '$DB_USER'@'localhost'; FLUSH PRIVILEGES;" 2>/dev/null; then
            log ERROR "Failed to create MySQL user $DB_USER"
            rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE"
            exit 1
	fi
    else
	log INFO "User $DB_USER already exists, ensuring privileges"
	if ! mysql -h "$DB_HOST" -u "$MYSQL_ROOT_USER" -p"$MYSQL_ROOT_PASSWORD" -e "GRANT ALL PRIVILEGES ON $DB_NAME.* TO '$DB_USER'@'localhost'; FLUSH PRIVILEGES;" 2>/dev/null; then
            log ERROR "Failed to update privileges for $DB_USER"
            rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE"
            exit 1
	fi
    fi

    # Create database if it doesn't exist
    log INFO "Ensuring database $DB_NAME exists"
    if ! mysql -h "$DB_HOST" -u "$MYSQL_ROOT_USER" -p"$MYSQL_ROOT_PASSWORD" -e "CREATE DATABASE IF NOT EXISTS $DB_NAME;" 2>/dev/null; then
	log ERROR "Failed to create or verify database $DB_NAME"
	rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE"
	exit 1
    fi

    # Install the SQL dump into the database
    log INFO "Importing $DOWNLOAD_DIR/$EXTRACTED_FILE into $DB_NAME"
    if ! mysql -h "$DB_HOST" -u "$DB_USER" -p"$DB_PASSWORD" "$DB_NAME" < "$DOWNLOAD_DIR/$EXTRACTED_FILE"; then
	log ERROR "Failed to import $DOWNLOAD_DIR/$EXTRACTED_FILE into $DB_NAME"
	rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE"
	exit 1
    fi

    # Clean up
    log INFO "Removing $DOWNLOAD_DIR/$EXTRACTED_FILE"
    rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE"

    log INFO "Database import completed successfully"
}

if [ "$1" = "--init-sql" ]; then
    init_sql
    exit 0
fi

init_rdf() {
    # Check for required tools
    for cmd in guix; do
	if ! command -v "$cmd" &> /dev/null; then
            log ERROR "Required command '$cmd' not found"
            exit 1
	fi
    done

    log INFO "Please make sure your container is running for this to work"
    log INFO "This takes some time to run"
    # Check if directory exists and is accessible
    if [ -d "$BASE_DIR/var/lib/data" ]; then
        if [ -w "$BASE_DIR/var/lib/data" ]; then
	    log "DEBUG" "Directory exists and is writable: $BASE_DIR/var/lib/data"
        else
	    log "WARNING" "Directory exists but is not writable: $BASE_DIR/var/lib/data.  Making this writable"
	    sudo chown -R "$USER" "$BASE_DIR/var/lib/data"
        fi
        continue
    fi
    curr_dir="$PWD"
    cd "$BASE_DIR/gn-transform-databases"
    if ls $BASE_DIR/var/lib/data/*ttl >/dev/null 2>&1; then
	log INFO "Removing all the ttl files and generating them again"
	rm $BASE_DIR/var/lib/data/*ttl
    fi

    log INFO "Generating the ttl files"
    guix shell -m "manifest.scm" -- guile "generate-ttl-files.scm" \
	 --settings "$curr_dir/etc/conn.scm" --output "$BASE_DIR/var/lib/data"
    log INFO "Loading ttl files"
    guix shell guile-dbi -m "manifest.scm" -- guile load-rdf.scm \
	 "$curr_dir/etc/conn.scm"
    cd $curr_dir
}

if [ "$1" = "--init-rdf" ]; then
    init_rdf
    exit 0
fi

init_xapian() {
    # Check for required tools
    log INFO "Please make sure your container is running for this to work"
    log INFO "This takes some time to run"
    # Check if directory exists and is accessible
    if [ -d "$BASE_DIR/var/lib/xapian" ]; then
        if [ -w "$BASE_DIR/var/lib/xapian" ]; then
	    log "DEBUG" "Directory exists and is writable: $BASE_DIR/var/lib/xapian"
        else
	    log "WARNING" "Directory exists but is not writable: $BASE_DIR/var/lib/xapian.  Making this writable"
	    sudo chown -R "$USER" "$BASE_DIR/var/lib/xapian"
        fi
        continue
    fi
    # Check if build directory exists
    if [ ! -f "$BASE_DIR/var/lib/xapian/build" ]; then
        rm -rf "$BASE_DIR/var/lib/xapian/build"
    fi

    env PYTHONPATH="$BASE_DIR/genenetwork3/" guix shell python-wrapper genenetwork3 \
	--share="$BASE_DIR/var/lib/xapian"  -- \
	"$BASE_DIR/genenetwork3/scripts/index-genenetwork" create-xapian-index \
	"$BASE_DIR/var/lib/xapian/build" \
	"mysql://webqtlout:webqtlout@localhost/db_webqtl_local?unix_socket=/run/mysqld/mysqld.sock&charset=utf8" \
	"http://localhost:7082/sparql"
    mv "$BASE_DIR/var/lib/xapian/build/*" "$BASE_DIR/var/lib/xapian/" \
	&& rmdir "$BASE_DIR/var/lib/xapian/build/"
    log INFO "Please restart the container to set the correct permissions"
}

if [ "$1" = "--init-xapian" ]; then
    init_xapian
    exit 0
fi


# Function to handle yes/no prompts
prompt_yes_no() {
    local prompt="$1"
    while true; do
        read -p "$prompt (yes/no): " response
        case "$response" in
            [Yy][Ee][Ss]|[Yy] ) return 0 ;;
            [Nn][Oo]|[Nn] ) return 1 ;;
            * ) echo "Please answer 'yes' or 'no'." ;;
        esac
    done
}

# Main tutorial function
run_beginner_setup_tutorial() {
    clear
    # Step 1: Initialize Container
    echo "Step 1: Setting Up the Container"
    echo "--------------------------------"
    echo "Before we begin, make sure you are using the correct guix-profile that has:"
    echo ""
    echo "     guix-bioinformatics"
    echo ""
    echo "Otherwise, I will terminate early.  If you don't know how to do that, read:"
    echo ""
    echo "     https://issues.genenetwork.org/topics/guix/guix-profiles"
    echo ""
    echo "This step prepares the container environment where GeneNetwork runs."
    echo "It ensures all necessary files, folders, and configurations are in place."
    echo ""
    echo "This step is similar to running:"
    echo ""
    echo "./genenetwork-local-container.sh --init-container"
    echo ""
    echo "NOTE: If you have any of the following projects:"
    echo "           genenetwork2"
    echo "           genenetwork3"
    echo "           gn-uploader"
    echo ""
    echo "Move/copy them to $BASE_DIR.  This is where'll you'll be hacking"
    echo "on them from.  Because of how we mount things inside the container,"
    echo "make sure the names appear as above."
    echo ""
    echo "Now, some things to note.  AI search won't work.  To get this working, if you want so,"
    echo "Get into the container, and modify FAHAMU_AUTH_TOKEN in:"
    echo "     /etc/genenetwork/conf/gn3/secrets.py"
    echo ""
    echo "Similarly, e-mail functionality ala resetting passwords or confirming a new user"
    echo "won't work unless you modify:"
    echo "  SMTP_HOST = 'XXXX'"
    echo "  SMTP_USER = 'XXXX'"
    echo "  SMTP_PASSWORD = 'XXXX'"
    echo "  SMTP_PORT = 'XXXX'"
    echo "  EMAIL_ADDRESS = 'XXXX'"
    echo "  EMAIL_DISPLAY_NAME = 'XXXX'"
    echo "inside:"
    echo "     /etc/genenetwork/conf/gn-auth/secrets.py"
    echo ""
    if prompt_yes_no "Would you like to set up the container now?"; then
        init_container
	clear
        echo "Container setup complete!"
	echo ""
	echo "Right now you have a working container.  You need to set-up sql, upload rdf data"
	echo "and build a xapian index to have a fully functioning system akin to production and"
	echo "our test environment."
	echo ""
    else
	clear
        echo "Skipping container setup. Moving to the next step."
    fi
    echo ""

    # Step 2: Initialize SQL Database
    echo "Step 2: Setting Up the SQL Database"
    echo "-----------------------------------"
    echo "Please make sure you have a working MariaDB installation on your Linux system."
    echo ""
    echo "This step creates and configures the database for storing GeneNetwork data."
    echo ""
    echo "It sets up tables and initial data needed for Genenetwork to run"
    echo ""
    echo "This step is similar to running:"
    echo "./genenetwork-local-container.sh --init-sql"
    echo ""
    echo "Make sure you have a running mysql instance for this to work"
    echo ""
    if prompt_yes_no "Would you like to set up the database now?"; then
        init_sql
	clear
        echo "Database setup complete!"
    else
	clear
        echo "Skipping database setup. Moving to the next step: Importing RDF"
    fi
    echo ""

    # Step 3: Initialize RDF
    echo ""
    echo "Step 3: Importing RDF into your local set-up"
    echo "---------------------------------------------"
    echo "This step adds RDF (Resource Description Framework) data."
    echo ""
    echo "RDF helps organize and link data for GeneNetwork."
    echo ""
    echo "IMPORTANT. This step requires you to have a running container instance."
    echo "           Otherwise, it will fail."
    echo "To run your container, in a different shell, run:"
    echo "sudo /usr/local/bin/genenetwork-local-container"
    echo ""
    echo "This step is similar to running:"
    echo "./genenetwork-local-container.sh --init-rdf"
    echo ""
    echo "Make sure your container, if not, is running for this to work:"
    echo ""
    echo "sudo /usr/local/bin/genenetwork-local-container"
    if prompt_yes_no "Would you like to set up RDF now?"; then
        init_rdf
	clear
        echo "RDF setup complete!"
    else
	clear
        echo "Skipping RDF setup."
    fi
    echo ""

    # Step 4: Initialize XAPIAN
    clear
    echo "Step 3: Setting up XAPIAN search locally"
    echo "---------------------------------------------"
    echo "This indexes all your data from GeneNetwork and indexes it using XAPIAN"
    echo ""
    echo "Read more here:"
    echo "https://issues.genenetwork.org/topics/xapian/xapian-search"
    echo ""
    echo "IMPORTANT. This step requires you to have a running container instance."
    echo "           Otherwise, it will fail."
    echo "           To run your container, in a different shell, run:"
    echo "           sudo /usr/local/bin/genenetwork-local-container"
    echo ""
    echo "This step is similar to running:"
    echo "./genenetwork-local-container.sh --init-xapian"
    echo ""
    echo "Make sure your container, if not, is running for this to work:"
    echo ""
    echo "sudo /usr/local/bin/genenetwork-local-container"
    if prompt_yes_no "Would you like to build the xapian index now?"; then
        init_xapian
	clear
        echo "XAPIAN setup complete!"
    else
	clear
        echo "Skipping RDF setup."
    fi
    echo ""

    # Completion Message
    echo "============================================================="
    echo "Congratulations! You've completed the GeneNetwork Beginner Setup Tutorial!"
    echo "============================================================="
    echo "You may have skipped some steps. To complete them, run the tutorial again."
    echo "Your environment is ready to the extent you chose to set it up."
    echo "If you run your container, you can access the different web-services at:"
    echo "gn-guile     : localhost:8091"
    echo "genenetwork2 : localhost:8082"
    echo "genenetwork3 : localhost:8083"
    echo "gn-uploader  : localhost:8085"
    echo "sparql web ui: localhost:7082/sparql"
    echo ""
    echo "To access virtuoso back-end service, run:"
    echo "guix shell virtuoso-ose isql -- 7081"
    echo ""
    echo "To login in gn-uploader/genenetwork2, use the following credentials:"
    echo "  Email: test@development.user"
    echo "  Password: testpasswd"
    exit 0
}

# Check for --beginner-set-up flag or run tutorial interactively
if [ "$1" = "--beginner-set-up" ]; then
    # Interactive mode: run the tutorial
    run_beginner_setup_tutorial
    exit 0
fi