Upgrade Dataverse v5.14 to v6.0

upgrade_5_14_to_6_0.sh

#!/bin/bash

# Globals
DOMAIN="dataverse-clone.mse.jhu.edu"
PAYARA_OLD="/usr/local/payara5"
PAYARA_NEW="/usr/local/payara6"
JAVA_UPGRADE_SCRIPT_URL="https://gist.github.com/DonRichards/cb992523a5ec588f1fb978d752d0d030/raw/upgrade_java.sh"
PAYARA_ZIP_URL="https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip"
DATAVERSE_WAR_URL="https://github.com/IQSS/dataverse/releases/download/v6.0/dataverse-6.0.war"
SOLR_TAR_URL="https://archive.apache.org/dist/solr/solr/9.3.0/solr-9.3.0.tgz"
DVINSTALL_ZIP_URL="https://github.com/IQSS/dataverse/releases/download/v6.0/dvinstall.zip"

DATAVERSE_USER="dataverse"
SOLR_USER="solr"
CURRENT_VERSION="5.14"
TARGET_VERSION="6.0"
PAYARA_SERVICE_FILE="$(systemctl show -p FragmentPath payara.service | cut -d'=' -f2)"
if [[ -z "$PAYARA_SERVICE_FILE" ]]; then
    printf " - Error: payara.service file path not found.\n" >&2
    return 1
fi
SOLR_SERVICE_FILE="$(systemctl show -p FragmentPath solr.service | cut -d'=' -f2)"
if [[ -z "$SOLR_SERVICE_FILE" ]]; then
    printf " - Error: solr.service file path not found.\n" >&2
    return 1
fi

COUNTER_DAILY_SCRIPT="/etc/cron.daily/counter_daily.sh"
COUNTER_PROCESSOR_DIR="/usr/local/counter-processor-0.1.04"
DATAVERSE_FILE_DIRECTORY="/mnt/dvn/dv-content"

MAIL_HOST="your_smtp_server"
MAIL_USER="your_mail_user"
MAIL_FROM_ADDRESS="your_from_address"

# Ensure the script is not run as root
if [[ $EUID -eq 0 ]]; then
    printf "Please do not run this script as root.\n" >&2
    printf "This script runs several commands with sudo from within functions.\n" >&2
    exit 1
fi

# Function to undeploy the current Dataverse version
undeploy_dataverse() {
    echo " - Undeploying current Dataverse version..."
    if sudo -u "$DATAVERSE_USER" "$PAYARA_OLD/bin/asadmin" list-applications | grep -q "dataverse-$CURRENT_VERSION"; then
        if ! sudo -u "$DATAVERSE_USER" "$PAYARA_OLD/bin/asadmin" undeploy "dataverse-$CURRENT_VERSION"; then
            echo " - Error undeploying Dataverse $CURRENT_VERSION." >&2
            return 1
        fi
    else
        echo " - Dataverse $CURRENT_VERSION is not currently deployed. Skipping undeploy step."
    fi
}

# Function to stop Payara
stop_payara() {
    local payara_path="$1"
    echo " - Stopping Payara at $payara_path..."
    if pgrep -f "payara" > /dev/null; then
        if ! sudo -u "$DATAVERSE_USER" "$payara_path/bin/asadmin" stop-domain; then
            echo " - Error stopping Payara." >&2
            return 1
        fi
    else
        echo " - Payara is already stopped."
    fi
}

# Function to stop Solr
stop_solr() {
    echo " - Stopping Solr service..."
    if pgrep -f "solr" > /dev/null; then
        if ! sudo systemctl stop solr; then
            echo " - Error stopping Solr." >&2
            return 1
        fi
    else
        echo " - Solr is already stopped."
    fi
}

# Waiting for payara to come back up.
wait_for_site() {
    local url="https://${DOMAIN}/dataverse/root?q="
    local response_code

    printf " - Waiting for site to become available...\n"
    
    while true; do
        # Get HTTP response code
        response_code=$(curl -o /dev/null -s -w "%{http_code}" "$url")

        if [[ "$response_code" -eq 200 ]]; then
            printf " - Site is up (HTTP 200 OK).\n"
            break
        else
            printf "\r - Waiting... (HTTP response: %s)" "$response_code"
        fi

        # Wait 1 seconds before checking again
        sleep 1
    done
}

# Function to upgrade Java
upgrade_java() {
    echo " - Upgrading Java..."
    cd /tmp || return 1
    if ! curl -L -O "$JAVA_UPGRADE_SCRIPT_URL"; then
        echo " - Error downloading Java upgrade script." >&2
        return 1
    fi
    chmod +x upgrade_java.sh
    if ! ./upgrade_java.sh; then
        echo " - Error executing Java upgrade script." >&2
        return 1
    fi
    rm -f upgrade_java.sh
}

# Function to download Payara 6
download_payara() {
    echo " - Downloading Payara 6..."
    cd /tmp || return 1
    if ! curl -L -O "$PAYARA_ZIP_URL"; then
        echo " - Error downloading Payara 6." >&2
        return 1
    fi
}

# Function to install Payara 6
install_payara() {
    echo " - Installing Payara 6..."
    if ! sudo unzip -o "payara-6.2023.8.zip" -d /usr/local/; then
        echo " - Error unzipping Payara 6." >&2
        return 1
    fi
    sudo ln -sf /usr/local/payara6 /usr/local/payara
    rm -f "payara-6.2023.8.zip"
}

# Function to configure Payara permissions
configure_payara_permissions() {
    echo " - Configuring Payara permissions..."
    if ! sudo chown -R "$DATAVERSE_USER" /usr/local/payara6; then
        echo " - Error setting ownership for Payara 6." >&2
        return 1
    fi
}

# Function to migrate domain.xml and update configurations
migrate_domain_xml() {
    local script_dir
    script_dir=$(dirname "$(readlink -f "$0")")
    local domain_xml_local="$script_dir/6_0_domain.xml"
    local domain_xml_new="$PAYARA_NEW/glassfish/domains/domain1/config/domain.xml"
    local domain_xml_old="$PAYARA_OLD/glassfish/domains/domain1/config/domain.xml"
    local backup_file="${domain_xml_new}.orig"
    
    # echo " - Checking for $domain_xml_local..."
    # if [ ! -f "$domain_xml_local" ]; then
    #     echo " - Local domain.xml not found, exiting."
    #     return 1
    # fi
    
    echo " - Migrating domain.xml and updating configurations..."

    # # Backup the new domain.xml
    # if ! sudo cp "$domain_xml_new" "$backup_file"; then
    #     echo " - Error backing up new domain.xml." >&2
    #     return 1
    # fi

    # Extract JVM options from the old domain.xml
    local jvm_options
    jvm_options=$(sudo grep -E 'dataverse|doi' "$domain_xml_old" | grep '<jvm-options>' | sed 's/.*<jvm-options>\(.*\)<\/jvm-options>.*/\1/')

    # Use awk to insert JVM options safely into domain.xml
    sudo awk -v jvm_options="$jvm_options" '
    /<\/java-config>/ {
        print "<jvm-options>" jvm_options "</jvm-options>"
    }
    { print }
    ' "$domain_xml_new" | sudo tee "$domain_xml_new.tmp" > /dev/null

    if [ $? -ne 0 ]; then
        echo " - Error inserting JVM options into new domain.xml." >&2
        return 1
    fi

    # Move the tmp file to the correct location with sudo
    if ! sudo mv "$domain_xml_new.tmp" "$domain_xml_new"; then
        echo " - Error replacing the domain.xml file." >&2
        return 1
    fi

    # Update file directory paths
    if [ -z "$DATAVERSE_FILE_DIRECTORY" ]; then
        echo " - Error: DATAVERSE_FILE_DIRECTORY is not set." >&2
        return 1
    fi
    if ! sudo sed -i "s|-Ddataverse.files.file.directory=.*|-Ddataverse.files.file.directory=$DATAVERSE_FILE_DIRECTORY|" "$domain_xml_new"; then
        echo " - Error updating file directory path in domain.xml." >&2
        return 1
    fi

    echo " - domain.xml successfully migrated and updated."
}


# Function to migrate jhove files
migrate_jhove_files() {
    echo " - Migrating jhove configuration files..."
    local config_dir_old="$PAYARA_OLD/glassfish/domains/domain1/config"
    local config_dir_new="$PAYARA_NEW/glassfish/domains/domain1/config"

    if ! sudo rsync -av "$config_dir_old"/jhove* "$config_dir_new/"; then
        printf " - Error migrating jhove files.\n" >&2
        return 1
    fi

    # Update jhove.conf to reference payara6
    if ! sudo sed -i 's|payara5|payara6|' "$config_dir_new/jhove.conf"; then
        echo " - Error updating jhove.conf." >&2
        return 1
    fi

    if ! sudo chown -R "$DATAVERSE_USER" "$config_dir_new"/jhove*; then
        echo " - Error setting ownership for jhove files." >&2
        return 1
    fi
}

# Function to migrate logos
migrate_logos() {
    echo " - Migrating logos..."
    local docroot_old="$PAYARA_OLD/glassfish/domains/domain1/docroot"
    local docroot_new="$PAYARA_NEW/glassfish/domains/domain1/docroot"

    if ! sudo -u "$DATAVERSE_USER" rsync -av "$docroot_old/logos/" "$docroot_new/logos/"; then
        echo " - Error migrating logos." >&2
        return 1
    fi
}

# Function to migrate MDC logs
migrate_mdc_logs() {
    echo " - Migrating MDC logs..."
    local logs_old="$PAYARA_OLD/glassfish/domains/domain1/logs/mdc"
    local logs_new="$PAYARA_NEW/glassfish/domains/domain1/logs/mdc"

    if ! sudo rsync -av "$logs_old" "$logs_new"; then
        echo " - Error migrating MDC logs." >&2
        return 1
    fi
}

# Function to update cron jobs and counter processor paths
update_cron_jobs() {
    echo " - Updating cron jobs and counter processor paths..."
    if ! sudo sed -i 's|payara5|payara6|' "$COUNTER_DAILY_SCRIPT"; then
        echo " - Error updating $COUNTER_DAILY_SCRIPT." >&2
        return 1
    fi

    if ! sudo find "$COUNTER_PROCESSOR_DIR" -type f -exec sed -i 's|/payara5/|/payara6/|g' {} +; then
        echo " - Error updating counter processor paths." >&2
        return 1
    fi
}

# Function to update Payara service
update_payara_service() {
    local backup_file="$PAYARA_SERVICE_FILE.bak"

    printf " - Updating Payara service...\n"

    # Validate the service file exists
    if [[ ! -f "$PAYARA_SERVICE_FILE" ]]; then
        printf " - Service file not found: %s\n" "$PAYARA_SERVICE_FILE" >&2
        return 1
    fi

    # Create a backup of the service file
    if ! sudo cp "$PAYARA_SERVICE_FILE" "$backup_file"; then
        printf " - Error creating backup of %s.\n" "$PAYARA_SERVICE_FILE" >&2
        return 1
    fi

    # Perform the sed replacement
    if ! sudo sed -i 's|payara5|payara6|' "$PAYARA_SERVICE_FILE"; then
        printf " - Error updating %s.\n" "$PAYARA_SERVICE_FILE" >&2
        return 1
    fi

    # Reload systemd and restart the service with proper error handling
    if ! sudo systemctl daemon-reload; then
        printf " - Error reloading systemd daemon.\n" >&2
        return 1
    fi

    if ! sudo systemctl stop payara; then
        printf " - Error stopping Payara service.\n" >&2
        return 1
    fi

    if ! sudo systemctl start payara; then
        printf " - Error starting Payara service.\n" >&2
        return 1
    fi

    printf " - Payara service updated and restarted successfully.\n"
    return 0
}

# Function to start Payara 6
start_payara6() {
    echo " - Starting Payara 6..."
    if ! sudo systemctl start payara; then
        echo " - Error starting Payara 6." >&2
        return 1
    fi
}

# Function to create JavaMail resource
create_javamail_resource() {
    echo " - Creating JavaMail resource..."
    local output
    if ! output=$(sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" create-javamail-resource --mailhost "$MAIL_HOST" --mailuser "$MAIL_USER" --fromaddress "$MAIL_FROM_ADDRESS" mail/notifyMailSession 2>&1); then
        if [[ "$output" == *"already exists with resource-ref"* ]]; then
            echo " - JavaMail resource already exists. Proceeding..."
        else
            echo " - Error creating JavaMail resource: $output" >&2
            return 1
        fi
    fi
}

# Function to create password aliases
create_password_aliases() {
    echo " - Checking existing password aliases..."

    # Check for existing aliases
    local alias_list
    alias_list=$(sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" list-password-aliases)

    # Flags to track whether we need to create aliases
    local db_alias_exists=false
    local doi_alias_exists=false

    # Check if dataverse.db.password alias exists
    if echo "$alias_list" | grep -q "dataverse.db.password"; then
        echo " - Database password alias 'dataverse.db.password' already exists."
        db_alias_exists=true
    fi

    # Check if doi_password_alias alias exists
    if echo "$alias_list" | grep -q "doi_password_alias"; then
        echo " - DOI password alias 'doi_password_alias' already exists."
        doi_alias_exists=true
    fi

    # If both aliases exist, no need to proceed further
    if $db_alias_exists && $doi_alias_exists; then
        echo " - Both password aliases already exist. No need to create new ones."
        return 0
    fi

    # Create missing database password alias
    if ! $db_alias_exists; then
        read -s -p "Enter database password: " DB_PASSWORD
        echo
        if [[ -z "$DB_PASSWORD" ]]; then
            echo " - Error: Database password cannot be blank." >&2
            return 1
        fi

        # Write to temporary file and create alias
        echo "AS_ADMIN_ALIASPASSWORD=$DB_PASSWORD" > /tmp/dataverse.db.password.txt
        if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" create-password-alias dataverse.db.password --passwordfile /tmp/dataverse.db.password.txt; then
            echo " - Error creating database password alias." >&2
            rm -f /tmp/dataverse.db.password.txt
            return 1
        fi
        rm -f /tmp/dataverse.db.password.txt
        echo " - Database password alias 'dataverse.db.password' created successfully."
    else
    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" update-password-alias dataverse.db.password; then
            echo " - Error creating database password alias." >&2
            rm -f /tmp/dataverse.db.password.txt
            return 1
        fi
        echo " - Database password alias 'dataverse.db.password' updated successfully."
    fi

    # Create missing DOI password alias (optional)
    if ! $doi_alias_exists; then
        read -s -p "Enter DOI password (if applicable, or press Enter to skip): " DOI_PASSWORD
        echo
        if [[ -n "$DOI_PASSWORD" ]]; then
            echo "AS_ADMIN_ALIASPASSWORD=$DOI_PASSWORD" > /tmp/dataverse.doi.password.txt
            if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" create-password-alias doi_password_alias --passwordfile /tmp/dataverse.doi.password.txt; then
                echo " - Error creating DOI password alias." >&2
                rm -f /tmp/dataverse.doi.password.txt
                return 1
            fi
            rm -f /tmp/dataverse.doi.password.txt
            echo " - DOI password alias 'doi_password_alias' created successfully."
        else
            echo " - Skipping DOI password alias creation."
        fi
    fi

    # Final check to ensure both aliases are created
    alias_list=$(sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" list-password-aliases)
    if ! echo "$alias_list" | grep -q "dataverse.db.password"; then
        echo " - Error: Database password alias was not created." >&2
        return 1
    fi
    if ! echo "$alias_list" | grep -q "doi_password_alias"; then
        echo " - Error: DOI password alias was not created." >&2
        return 1
    fi

    echo " - All required password aliases are set."
}



# Function to create JVM options and restart Payara
create_jvm_options() {
    echo " - Creating JVM options..."
    local output
    if ! output=$(sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED 2>&1); then
        if [[ "$output" == *"already exists in the configuration"* ]]; then
            echo " - JVM option already exists. Proceeding..."
        else
            echo " - Error creating JVM options: $output" >&2
            return 1
        fi
    fi

    echo " - Restarting Payara 6..."
    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" stop-domain; then
        echo " - Error stopping Payara 6." >&2
        return 1
    fi
    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" start-domain; then
        echo " - Error starting Payara 6." >&2
        return 1
    fi
}


# Function to create network listener
create_network_listener() {
    echo " - Creating network listener..."
    local output
    if ! output=$(sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" create-network-listener --protocol http-listener-1 --listenerport 8009 --jkenabled true jk-connector 2>&1); then
        if [[ "$output" == *"already exists"* ]]; then
            echo " - Network listener 'jk-connector' already exists. Proceeding..."
        else
            echo " - Error creating network listener: $output" >&2
            return 1
        fi
    fi
}

# Function to deploy Dataverse
deploy_dataverse() {
    echo " - Deploying Dataverse..."
    cd /tmp || return 1
    if ! wget "$DATAVERSE_WAR_URL"; then
        echo " - Error downloading Dataverse WAR file." >&2
        return 1
    fi

    if ! sudo cp "dataverse-$TARGET_VERSION.war" "/home/$DATAVERSE_USER/"; then
        echo " - Error copying WAR file to /home/$DATAVERSE_USER/." >&2
        rm -f "dataverse-$TARGET_VERSION.war"
        return 1
    fi
    sudo chown "$DATAVERSE_USER:" "/home/$DATAVERSE_USER/dataverse-$TARGET_VERSION.war"

    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" deploy "/home/$DATAVERSE_USER/dataverse-$TARGET_VERSION.war"; then
        if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" deploy "dataverse-$TARGET_VERSION"; then
            echo -e " - Error deploying Dataverse WAR file.\n" >&2
            rm -f "dataverse-$TARGET_VERSION.war"
            return 1
        fi
    fi
    rm -f "dataverse-$TARGET_VERSION.war"
}

# Function to check Dataverse version
check_dataverse_version() {
    echo " - Checking Dataverse version..."
    local version
    version=$(curl -s "http://localhost:8080/api/info/version" | grep -oP '\d+\.\d+')
    if [ "$version" == "$TARGET_VERSION" ]; then
        echo " - Dataverse upgraded to version $TARGET_VERSION successfully."
    else
        echo " - Dataverse version check failed. Expected $TARGET_VERSION, got $version." >&2
        return 1
    fi
}

# Function to restart Payara 6
restart_payara6() {
    echo " - Restarting Payara 6..."
    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" stop-domain; then
        echo " - Error stopping Payara 6." >&2
        return 1
    fi
    if ! sudo -u "$DATAVERSE_USER" "$PAYARA_NEW/bin/asadmin" start-domain; then
        echo " - Error starting Payara 6." >&2
        return 1
    fi
}

# Function to download dvinstall
download_dvinstall() {
    echo " - Downloading dvinstall..."
    cd /tmp || return 1
    if ! wget "$DVINSTALL_ZIP_URL"; then
        echo " - Error downloading dvinstall.zip." >&2
        return 1
    fi
    if ! unzip -o dvinstall.zip; then
        echo " - Error unzipping dvinstall.zip." >&2
        rm -f dvinstall.zip
        return 1
    fi
    rm -f dvinstall.zip
}

# Function to upgrade Solr
upgrade_solr() {
    echo " - Upgrading Solr..."
    if ! sudo mv /usr/local/solr "/usr/local/solr-8.11.1"; then
        echo " - Error moving old Solr directory." >&2
        return 1
    fi

    cd /tmp || return 1
    if ! wget "$SOLR_TAR_URL"; then
        echo " - Error downloading Solr tarball." >&2
        return 1
    fi

    if ! tar xvzf "solr-9.3.0.tgz"; then
        echo " - Error extracting Solr tarball." >&2
        rm -f "solr-9.3.0.tgz"
        return 1
    fi

    if ! sudo mv "solr-9.3.0" "/usr/local/solr-9.3.0"; then
        echo " - Error moving Solr directory." >&2
        rm -rf "solr-9.3.0"
        rm -f "solr-9.3.0.tgz"
        return 1
    fi
    rm -f "solr-9.3.0.tgz"

    if ! sudo ln -sf "/usr/local/solr-9.3.0" /usr/local/solr; then
        echo " - Error creating Solr symlink." >&2
        return 1
    fi
}

# Function to update Solr configurations
update_solr_configs() {
    echo " - Updating Solr configurations..."
    if ! sudo rsync -avz "/usr/local/solr/server/solr/configsets/_default/" "/usr/local/solr/server/solr/collection1"; then
        echo " - Error copying Solr configsets." >&2
        return 1
    fi

    if ! sudo rsync -avz /tmp/dvinstall/schema*.xml "/usr/local/solr/server/solr/collection1/conf/"; then
        echo " - Error copying Solr schema files." >&2
        return 1
    fi

    if ! sudo cp "/tmp/dvinstall/solrconfig.xml" "/usr/local/solr/server/solr/collection1/conf/solrconfig.xml"; then
        echo " - Error copying Solr solrconfig.xml." >&2
        return 1
    fi
}

# Function to update Jetty configuration
update_jetty_config() {
    echo " - Updating Jetty configuration..."
    local jetty_file="/usr/local/solr-9.3.0/server/etc/jetty.xml"

    if ! sudo sed -i 's/\(<Set name="requestHeaderSize">.*default="\)[^"]*\("\)/\1102400\2/' "$jetty_file"; then
        echo " - Error updating Jetty requestHeaderSize." >&2
        return 1
    fi
}

# Function to configure Solr core
configure_solr_core() {
    echo " - Configuring Solr core..."
    if ! sudo touch "/usr/local/solr/server/solr/collection1/core.properties"; then
        echo " - Error creating core.properties." >&2
        return 1
    fi

    echo "name=collection1" | sudo tee "/usr/local/solr/server/solr/collection1/core.properties" > /dev/null

    if ! sudo chown -R "$SOLR_USER:" "/usr/local/solr-9.3.0/"; then
        echo " - Error setting ownership for Solr directories." >&2
        return 1
    fi
}

# Function to update Solr service
update_solr_service() {
    echo " - Updating Solr service..."
    local solr_service_file="$SOLR_SERVICE_FILE"

    if ! sudo sed -i '/^WorkingDirectory *= */s|/usr/local/solr$|/usr/local/solr|' "$solr_service_file"; then
        echo " - Error updating WorkingDirectory in solr.service." >&2
        return 1
    fi

    if ! sudo sed -i '/^ExecStart *= */s|/usr/local/solr/bin/solr|/usr/local/solr/bin/solr|' "$solr_service_file"; then
        echo " - Error updating ExecStart in solr.service." >&2
        return 1
    fi

    if ! sudo sed -i '/^ExecStop *= */s|/usr/local/solr/bin/solr|/usr/local/solr/bin/solr|' "$solr_service_file"; then
        echo " - Error updating ExecStop in solr.service." >&2
        return 1
    fi

    sudo systemctl daemon-reload
}

# Function to start Solr service
start_solr_service() {
    echo " - Starting Solr service..."
    if ! sudo systemctl start solr; then
        echo " - Error starting Solr service." >&2
        return 1
    fi

    # Verify Solr is running
    if ! curl -s "http://localhost:8983/solr/collection1/schema/fields" > /dev/null; then
        echo " - Error: Solr is not responding as expected." >&2
        return 1
    fi
}

# Function to update Solr schema
update_solr_schema() {
    echo " - Updating Solr schema..."
    cd /tmp || return 1
    if ! wget "https://guides.dataverse.org/en/6.0/_downloads/1158e888bffd60c8a89df32fe90f8181/update-fields.sh"; then
        echo " - Error downloading update-fields.sh." >&2
        return 1
    fi

    sudo chown "$SOLR_USER:" update-fields.sh
    sudo chmod +x update-fields.sh

    if ! sudo yum install -y ed; then
        echo " - Error installing 'ed' editor." >&2
        return 1
    fi

    if ! sudo -u "$SOLR_USER" bash -c 'curl "http://localhost:8080/api/admin/index/solr/schema" | ./update-fields.sh /usr/local/solr/server/solr/collection1/conf/schema.xml'; then
        echo " - Error updating Solr schema." >&2
        return 1
    fi

    if ! sudo -u "$SOLR_USER" bash -c 'curl "http://localhost:8983/solr/admin/cores?action=RELOAD&core=collection1"'; then
        echo " - Error reloading Solr core." >&2
        return 1
    fi

    if ! curl -s "http://localhost:8080/api/admin/index" | jq > /dev/null; then
        echo " - Error verifying Solr index." >&2
        return 1
    fi
}
CPU_THRESHOLD=80  # High CPU usage threshold
CHECK_INTERVAL=5  # Seconds between checks

# Function to get current CPU usage
get_cpu_usage() {
    local cpu_idle; cpu_idle=$(top -bn1 | grep "Cpu(s)" | sed "s/.*, *\([0-9.]*\)%* id.*/\1/")
    printf "%.0f\n" "$(echo "100 - $cpu_idle" | bc)"
}

# Main function to monitor CPU usage
monitor_cpu() {
    while :; do
        local timestamp; timestamp=$(date '+%Y-%m-%d %H:%M:%S')
        local current_cpu; current_cpu=$(get_cpu_usage)
        
        printf "\r[%s] Dataverse is running several update tasks, CPU usage: %s%%" "$timestamp" "$current_cpu"
        
        if [[ $current_cpu -lt $CPU_THRESHOLD ]]; then
            printf "\n[%s] Task has completed. CPU usage is back to normal.\n" "$timestamp"
            return
        fi
        sleep "$CHECK_INTERVAL"
    done
}

# Main function
main() {
    # Ensure Payara environment variables are set
    export PAYARA="$PAYARA_NEW"

    echo -e "\nStep 1: Undeploy the existing Dataverse version"
    if ! undeploy_dataverse; then
        printf " - Error during undeploy.\n" >&2
        exit 1
    fi

    echo -e "\nStep 2: Stop Payara 5"
    if ! stop_payara "$PAYARA_OLD"; then
        printf " - Error stopping Payara 5.\n" >&2
        exit 1
    fi

    echo -e "\nStep 3: Stop Solr"
    if ! stop_solr; then
        printf " - Error stopping Solr.\n" >&2
        exit 1
    fi

    echo -e "\nStep 4: Upgrade Java"
    if ! upgrade_java; then
        printf " - Error upgrading Java.\n" >&2
        exit 1
    fi

    echo -e "\nStep 5: Download Payara 6"
    if ! download_payara; then
        printf " - Error downloading Payara 6.\n" >&2
        exit 1
    fi

    echo -e "\nStep 6: Install Payara 6"
    if ! install_payara; then
        printf " - Error installing Payara 6.\n" >&2
        exit 1
    fi

    echo -e "\nStep 7: Configure Payara permissions"
    if ! configure_payara_permissions; then
        printf " - Error configuring Payara permissions.\n" >&2
        exit 1
    fi

    echo -e "\nStep 8: Migrate domain.xml"
    if ! migrate_domain_xml; then
        printf " - Error migrating domain.xml.\n" >&2
        exit 1
    fi

    echo -e "\nStep 9: Migrate jhove files"
    if ! migrate_jhove_files; then
        printf " - Error migrating jhove files.\n" >&2
        exit 1
    fi

    echo -e "\nStep 10: Migrate logos"
    if ! migrate_logos; then
        printf " - Error migrating logos.\n" >&2
        exit 1
    fi

    echo -e "\nStep 11: Migrate MDC logs"
    if ! migrate_mdc_logs; then
        printf " - Error migrating MDC logs.\n" >&2
        exit 1
    fi

    echo -e "\nStep 12: Update cron jobs and counter processor paths"
    if ! update_cron_jobs; then
        printf " - Error updating cron jobs.\n" >&2
        exit 1
    fi

    echo -e "\nStep 13: Update Payara service"
    if ! update_payara_service; then
        printf " - Error updating Payara service.\n" >&2
        exit 1
    fi

    echo -e "\nStep 14: Start Payara 6"
    if ! start_payara6; then
        printf " - Error starting Payara 6.\n" >&2
        exit 1
    fi

    echo -e "\nStep 15: Create JavaMail resource"
    if ! create_javamail_resource; then
        printf " - Error creating JavaMail resource.\n" >&2
        exit 1
    fi

    echo -e "\nStep 16: Create password aliases"
    if ! create_password_aliases; then
        printf " - Error creating password aliases.\n" >&2
        exit 1
    fi

    echo -e "\nStep 17: Create JVM options and restart Payara"
    if ! create_jvm_options; then
        printf " - Error creating JVM options.\n" >&2
        exit 1
    fi

    echo -e "\nStep 18: Create network listener"
    if ! create_network_listener; then
        printf " - Error creating network listener.\n" >&2
        exit 1
    fi

    echo -e "\nStep 19: Deploy Dataverse"
    if ! deploy_dataverse; then
        printf " - Error deploying Dataverse.\n" >&2
        exit 1
    fi

    echo -e "\nWait for Payara to come up."
    wait_for_site

    echo -e "\nStep 11 2nd part: Migrate MDC logs"
    echo " - Setting MDC path in config"
    curl -X PUT -d "$logs_new" http://localhost:8080/api/admin/settings/:MDCLogPath || return 1

    echo -e "\nStep 20: Check Dataverse version"
    if ! check_dataverse_version; then
        printf " - Error checking Dataverse version.\n" >&2
        exit 1
    fi

    echo -e "\nStep 21: Restart Payara 6"
    if ! restart_payara6; then
        printf " - Error restarting Payara 6.\n" >&2
        exit 1
    fi

    echo -e "\nStep 22: Download dvinstall"
    if ! download_dvinstall; then
        printf " - Error downloading dvinstall.\n" >&2
        exit 1
    fi

    echo "Solr Step 1: Upgrade Solr"
    if ! upgrade_solr; then
        printf " - Error upgrading Solr.\n" >&2
        exit 1
    fi

    echo "Solr Step 2: Update Solr configurations"
    if ! update_solr_configs; then
        printf " - Error updating Solr configurations.\n" >&2
        exit 1
    fi

    echo "Solr Step 3: Update Jetty configuration"
    if ! update_jetty_config; then
        printf " - Error updating Jetty configuration.\n" >&2
        exit 1
    fi

    echo "Solr Step 4: Configure Solr core"
    if ! configure_solr_core; then
        printf " - Error configuring Solr core.\n" >&2
        exit 1
    fi

    echo "Solr Step 5: Update Solr service"
    if ! update_solr_service; then
        printf " - Error updating Solr service.\n" >&2
        exit 1
    fi

    echo "Solr Step 6: Start Solr service"
    if ! start_solr_service; then
        printf " - Error starting Solr service.\n" >&2
        exit 1
    fi

    echo "Solr Step 7: Update Solr schema"
    if ! update_solr_schema; then
        printf " - Error updating Solr schema.\n" >&2
        exit 1
    fi

    printf "\n\nUpgrade to Dataverse %s completed successfully.\n\n" "$TARGET_VERSION"

    # Not needed.
    monitor_cpu
}

# Run the main function
main "$@"