Upgrade Dataverse v6.1 to v6.2

upgrade_6_1_to_6_2.sh

#!/bin/bash
# Used release to generate this: https://github.com/IQSS/dataverse/releases/tag/v6.2

# Globals
DOMAIN="dataverse-clone.mse.jhu.edu"
PAYARA="/usr/local/payara"
SOLR_SCHEMA_URL="https://raw.githubusercontent.com/IQSS/dataverse/v6.2/conf/solr/9.3.0/schema.xml"
SOLR_SCHEMA_FILE=$(basename "$SOLR_SCHEMA_URL")
DATAVERSE_WAR_URL="https://github.com/IQSS/dataverse/releases/download/v6.2/dataverse-6.2.war"
DATAVERSE_WAR_FILE="/home/dataverse/dataverse-6.2.war"
DATAVERSE_WAR_HASH="d0c8c62025457e35333ec7c9bf896355ffeb3b6823020da5f53599b72f399d2e"
GEOSPATIAL_URL="https://github.com/IQSS/dataverse/releases/download/v6.2/geospatial.tsv"
GEOSPATIAL_FILE="/tmp/geospatial.tsv"
CITATION_URL="https://github.com/IQSS/dataverse/releases/download/v6.2/citation.tsv"
CITATION_FILE="/tmp/citation.tsv"
ASTROPHYSICS_URL="https://github.com/IQSS/dataverse/releases/download/v6.2/astrophysics.tsv"
ASTROPHYSICS_FILE="/tmp/astrophysics.tsv"
BIOMEDICAL_URL="https://github.com/IQSS/dataverse/releases/download/v6.2/biomedical.tsv"
BIOMEDICAL_FILE="/tmp/biomedical.tsv"
SOLR_FIELD_UPDATER_URL="https://raw.githubusercontent.com/IQSS/dataverse/refs/tags/v6.2/conf/solr/9.3.0/update-fields.sh"
SOLR_FIELD_UPDATER_FILE="/tmp/update-fields.sh"
DEPLOY_DIR="$PAYARA/glassfish/domains/domain1/generated"
CURRENT_VERSION="6.1"
TARGET_VERSION="6.2"
DATAVERSE_USER="dataverse"
BASHRC_FILE="/home/dataverse/.bashrc"
PAYARA_EXPORT_LINE="export PAYARA=\"$PAYARA\""
RATE_LIMIT_JSON_FILE="rate-limit-actions-setting.json"

# 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

check_current_version() {
    local version response
    response=$(sudo -u dataverse $PAYARA/bin/asadmin list-applications)

    # Check if "No applications are deployed to this target server" is part of the response
    if [[ "$response" == *"No applications are deployed to this target server"* ]]; then
        printf " - No applications are deployed to this target server. Assuming upgrade is needed.\n"
        return 0
    fi

    # If no such message, check the Dataverse version via the API
    version=$(curl -s "http://localhost:8080/api/info/version" | grep -oP '\d+\.\d+')

    # Check if the version matches the expected current version
    if [[ $version == "$CURRENT_VERSION" ]]; then
        return 0
    else
        printf " - Current Dataverse version is not %s. Upgrade cannot proceed.\n" "$CURRENT_VERSION" >&2
        return 1
    fi
}

# Function to undeploy the current Dataverse version
undeploy_dataverse() {
    if sudo -u dataverse $PAYARA/bin/asadmin list-applications | grep -q "dataverse-$CURRENT_VERSION"; then
        printf " - Undeploying current Dataverse version...\n"
        sudo -u dataverse $PAYARA/bin/asadmin undeploy dataverse-$CURRENT_VERSION || return 1
    else
        printf " - Dataverse is not currently deployed. Skipping undeploy step.\n"
    fi
}

# Function to stop Payara service
stop_payara() {
    if pgrep -f payara > /dev/null; then
        printf " - Stopping Payara service...\n"
        sudo systemctl stop payara || return 1
    else
        printf " - Payara is already stopped.\n"
    fi
}

stop_solr() {
    if pgrep -f solr > /dev/null; then
        printf " - Stopping Solr service...\n"
        sudo systemctl stop solr || return 1
    else
        printf " - Solr is already stopped.\n"
    fi
}

start_solr() {
    if ! pgrep -f solr > /dev/null; then
        printf " - Starting Solr service...\n"
        sudo systemctl start solr || return 1
    else
        printf " - Solr is already running.\n"
    fi
}

# Function to start Payara service
start_payara() {
    if ! pgrep -f payara > /dev/null; then
        printf " - Starting Payara service...\n"
        sudo systemctl start payara || return 1
    else
        printf " - Payara is already running.\n"
    fi
}

# Function to clean generated directory
clean_generated_dir() {
    if [[ -d "$DEPLOY_DIR" ]]; then
        printf " - Removing generated directory...\n"
        sudo rm -rf "$DEPLOY_DIR" || return 1
    else
        printf " - Generated directory already clean. Skipping.\n"
    fi
}

download_war_file() {
    if [[ -f "$DATAVERSE_WAR_FILE" ]]; then
        printf " - WAR file already exists at %s. Skipping download.\n" "$DATAVERSE_WAR_FILE"
        ACTUAL_HASH=$(sudo -u dataverse shasum -a 256 "$DATAVERSE_WAR_FILE" | awk '{print $1}')
        if [ "$ACTUAL_HASH" != "$DATAVERSE_WAR_HASH" ]; then
            echo "Hash mismatch!"
            rm -f $DATAVERSE_WAR_FILE
        else
            echo "Hash matches!"
            return 0
        fi
    fi
    printf " - WAR file not found or its hash didn't match. Downloading...\n"
    sudo rm -f "$DATAVERSE_WAR_FILE"
    if ! sudo -u dataverse curl -L -o "$DATAVERSE_WAR_FILE" "$DATAVERSE_WAR_URL"; then
        printf " - Error downloading the WAR file.\n" >&2
        return 1
    fi
    printf " - Download completed successfully.\n"
    sudo chown dataverse:dataverse $DATAVERSE_WAR_FILE
    ACTUAL_HASH=$(sudo -u dataverse shasum -a 256 "$DATAVERSE_WAR_FILE" | awk '{print $1}')
    if [ "$ACTUAL_HASH" != "$DATAVERSE_WAR_HASH" ]; then
        echo "Hash mismatch!"
        return 1
    else
        echo "Hash matches!"
    fi
}

download_solr_schema_file() {
    if [[ -f "$SOLR_SCHEMA_FILE" ]]; then
        printf " - SOLR_SCHEMA file already exists at %s. Skipping download.\n" "$SOLR_SCHEMA_FILE"
    else
        printf " - SOLR_SCHEMA file not found. Downloading...\n"
        if curl -L -o "$SOLR_SCHEMA_FILE" "$SOLR_SCHEMA_URL"; then
            printf " - SOLR_SCHEMA file downloaded successfully to %s\n" "$SOLR_SCHEMA_FILE"
        else
            printf " - Error downloading the SOLR_SCHEMA file. Exiting script.\n"
            return 1
        fi
    fi
}
update_solr_schema_file() {
    if [[ -f "$SOLR_SCHEMA_FILE" ]]; then
        printf " - Solr schema file found. Uploading...\n"
        sudo cp /usr/local/solr/server/solr/collection1/conf/schema.xml /usr/local/solr/server/solr/collection1/conf/schema.xml_$(date +"%Y%m%d") || return 1
        sudo chown solr:solr $SOLR_SCHEMA_FILE || return 1
        if ! sudo cp $SOLR_SCHEMA_FILE /usr/local/solr/server/solr/collection1/conf/schema.xml ; then
            printf " - Error copying with the Solr schema file.\n" >&2
            return 1
        fi
        printf " - Update completed successfully.\n"
        sudo rm -f $SOLR_SCHEMA_FILE
    else
        printf " - Solr schema file is missing at %s.\n" "$SOLR_SCHEMA_FILE"
        return 1
    fi
}

download_geospatial_file() {
    if [[ -f "$GEOSPATIAL_FILE" ]]; then
        printf " - Geospatial file already exists at %s. Skipping download.\n" "$GEOSPATIAL_FILE"
    else
        printf " - Geospatial file not found. Downloading...\n"
        if sudo -u dataverse bash -c "curl -L -o \"$GEOSPATIAL_FILE\" \"$GEOSPATIAL_URL\""; then
            printf " - Geospatial file downloaded successfully to %s\n" "$GEOSPATIAL_FILE"
        else
            printf " - Error downloading the Geospatial file. Exiting script.\n" >&2
            return 1
        fi
    fi
}

update_geospatial_metadata_block() {
    if [[ -f "$GEOSPATIAL_FILE" ]]; then
        printf " - Geospatial file found. Uploading...\n"
        
        # Capture the curl output
        local response
        response=$(sudo -u dataverse curl -s http://localhost:8080/api/admin/datasetfield/load \
            -H "Content-type: text/tab-separated-values" \
            -X POST --upload-file "$GEOSPATIAL_FILE")

        # Check if "The requested resource is not available" is in the response
        if echo "$response" | grep -q "The requested resource is not available"; then
            printf " - Error: The requested resource is not available.\n" >&2
            return 1
        fi

        # Check for any other curl errors
        if [[ $? -ne 0 ]]; then
            printf " - Error updating with the Geospatial file.\n" >&2
            return 1
        fi

        printf " - Update completed successfully.\n"
        sudo rm -f "$GEOSPATIAL_FILE"
    else
        printf " - Geospatial file is missing at %s.\n" "$GEOSPATIAL_FILE"
        return 1
    fi
}

download_citation_file() {
    if [[ -f "$CITATION_FILE" ]]; then
        printf " - Citation file already exists at %s. Skipping download.\n" "$CITATION_FILE"
    else
        printf " - Citation file not found. Downloading...\n"
        if sudo -u dataverse bash -c "curl -L -o \"$CITATION_FILE\" \"$CITATION_URL\""; then
            printf " - Citation file downloaded successfully to %s\n" "$CITATION_FILE"
        else
            printf " - Error downloading the Citation file. Exiting script.\n"
            return 1
        fi
    fi
}

update_citation_metadata_block() {
    if [[ -f "$CITATION_FILE" ]]; then
        printf " - Citation file found. Uploading...\n"
        
        # Capture the curl output
        local response
        response=$(sudo -u dataverse curl -s http://localhost:8080/api/admin/datasetfield/load \
            -H "Content-type: text/tab-separated-values" \
            -X POST --upload-file "$CITATION_FILE")

        # Check if "The requested resource is not available" is in the response
        if echo "$response" | grep -q "The requested resource is not available"; then
            printf " - Error: The requested resource is not available.\n" >&2
            return 1
        fi

        # Check for any other curl errors
        if [[ $? -ne 0 ]]; then
            printf " - Error updating with the Citation file.\n" >&2
            return 1
        fi

        printf " - Update completed successfully.\n"
        sudo rm -f "$CITATION_FILE"
    else
        printf " - Citation file is missing at %s.\n" "$CITATION_FILE"
        return 1
    fi
}

download_astrophysics_file() {
    if [[ -f "$ASTROPHYSICS_FILE" ]]; then
        printf " - ASTROPHYSICS file already exists at %s. Skipping download.\n" "$ASTROPHYSICS_FILE"
    else
        printf " - ASTROPHYSICS file not found. Downloading...\n"
        if sudo -u dataverse bash -c "curl -L -o \"$ASTROPHYSICS_FILE\" \"$ASTROPHYSICS_URL\""; then
            printf " - ASTROPHYSICS file downloaded successfully to %s\n" "$ASTROPHYSICS_FILE"
        else
            printf " - Error downloading the ASTROPHYSICS file. Exiting script.\n"
            return 1
        fi
    fi
}

update_astrophysics_metadata_block() {
    if [[ -f "$ASTROPHYSICS_FILE" ]]; then
        printf " - ASTROPHYSICS file found. Uploading...\n"
        
        # Capture the curl output
        local response
        response=$(sudo -u dataverse curl -s http://localhost:8080/api/admin/datasetfield/load \
            -H "Content-type: text/tab-separated-values" \
            -X POST --upload-file "$ASTROPHYSICS_FILE")

        # Check if "The requested resource is not available" is in the response
        if echo "$response" | grep -q "The requested resource is not available"; then
            printf " - Error: The requested resource is not available.\n" >&2
            return 1
        fi

        # Check for any other curl errors
        if [[ $? -ne 0 ]]; then
            printf " - Error updating with the ASTROPHYSICS file.\n" >&2
            return 1
        fi

        printf " - Update completed successfully.\n"
        sudo rm -f "$ASTROPHYSICS_FILE"
    else
        printf " - ASTROPHYSICS file is missing at %s.\n" "$ASTROPHYSICS_FILE"
        return 1
    fi
}

download_biomedical_file() {
    if [[ -f "$BIOMEDICAL_FILE" ]]; then
        printf " - BIOMEDICAL file already exists at %s. Skipping download.\n" "$BIOMEDICAL_FILE"
    else
        printf " - BIOMEDICAL file not found. Downloading...\n"
        if sudo -u dataverse bash -c "curl -L -o \"$BIOMEDICAL_FILE\" \"$BIOMEDICAL_URL\""; then
            printf " - BIOMEDICAL file downloaded successfully to %s\n" "$BIOMEDICAL_FILE"
        else
            printf " - Error downloading the BIOMEDICAL file. Exiting script.\n"
            return 1
        fi
    fi
}

update_biomedical_metadata_block() {
    if [[ -f "$BIOMEDICAL_FILE" ]]; then
        printf " - BIOMEDICAL file found. Uploading...\n"
        
        # Capture the curl output
        local response
        response=$(sudo -u dataverse curl -s http://localhost:8080/api/admin/datasetfield/load \
            -H "Content-type: text/tab-separated-values" \
            -X POST --upload-file "$BIOMEDICAL_FILE")

        # Check if "The requested resource is not available" is in the response
        if echo "$response" | grep -q "The requested resource is not available"; then
            printf " - Error: The requested resource is not available.\n" >&2
            return 1
        fi

        # Check for any other curl errors
        if [[ $? -ne 0 ]]; then
            printf " - Error updating with the BIOMEDICAL file.\n" >&2
            return 1
        fi

        printf " - Update completed successfully.\n"
        sudo rm -f "$BIOMEDICAL_FILE"
    else
        printf " - BIOMEDICAL file is missing at %s.\n" "$BIOMEDICAL_FILE"
        return 1
    fi
}

# Download and update Solr schema updater
download_solr_schema_updater() {
    if [[ -f "$SOLR_FIELD_UPDATER_FILE" ]]; then
        printf " - Solr Field Updater file already exists at %s. Skipping download.\n" "$SOLR_FIELD_UPDATER_FILE"
    else
        printf " - Solr Field Updater file not found. Downloading...\n"
        if sudo -u solr bash -c "curl -L -o \"$SOLR_FIELD_UPDATER_FILE\" \"$SOLR_FIELD_UPDATER_URL\""; then
            printf " - Solr Field Updater file downloaded successfully to %s\n" "$SOLR_FIELD_UPDATER_FILE"
        else
            printf " - Error downloading the Solr Field Updater file. Exiting script.\n"
            return 1
        fi
    fi
    if ! sudo chmod +x $SOLR_FIELD_UPDATER_FILE; then
        printf " - Error running chmod on $SOLR_FIELD_UPDATER_FILE"
        return 1
    fi
    if ! sudo chown solr:solr $SOLR_FIELD_UPDATER_FILE; then
        printf " - Error running chown on $SOLR_FIELD_UPDATER_FILE"
        return 1
    fi
}

update_solr_schema_updater() {
    if [[ -f "$SOLR_FIELD_UPDATER_FILE" ]]; then
        printf " - Solr file found. Uploading...\n"
        if ! sudo -u solr bash -c "curl http://localhost:8080/api/admin/index/solr/schema | bash $SOLR_FIELD_UPDATER_FILE /usr/local/solr/server/solr/collection1/conf/schema.xml" ; then
            printf " - Error updating with the Solr fields from update-fields script.\n" >&2
            return 1
        fi
        printf " - Update completed successfully.\n"
        sudo rm -f $SOLR_FIELD_UPDATER_FILE
    else
        printf " - Solr file is missing at %s.\n" "$SOLR_FIELD_UPDATER_FILE"
        return 1
    fi
    # New field that caused problems: Software Description "license" field.
    # This is a dropdown controlled vocab list.
    # Add this line to the schema.xml file.
    # <field name="license" type="keyword" indexed="true" stored="true" multiValued="false" />
    # <!-- JHU-managed fieldNames --> wasn't copied over

    if ! grep -q '<field name="license"' '/usr/local/solr/server/solr/collection1/conf/schema.xml'; then 
        sudo sed -i '/<!-- SCHEMA-FIELDS::END -->/a     <field name="license" type="string" indexed="true" stored="true" multiValued="false" />' /usr/local/solr/server/solr/collection1/conf/schema.xml
    fi
    # curl "http://localhost:8983/solr/admin/cores?action=STATUS"
}

deploy_new_version() {
    if ! sudo -u dataverse $PAYARA/bin/asadmin list-applications | grep -q "dataverse-$TARGET_VERSION"; then
        printf " - Deploying new Dataverse version...\n"
        sudo -u dataverse $PAYARA/bin/asadmin deploy "$DATAVERSE_WAR_FILE" || return 1
    else
        printf " - Dataverse version %s is already deployed. Skipping deployment.\n" "$TARGET_VERSION"
    fi
}

export_all_metadata() {
    sudo -u dataverse curl http://localhost:8080/api/admin/metadata/reExportAll || return 1
}

status_solr() {
    while true; do
        result=$(sudo -u solr bash -c "curl -s http://localhost:8983/solr/admin/cores?action=STATUS")

        # Check for initFailures
        init_failure=$(echo "$result" | jq -r '.initFailures.collection1 // empty')
        if [[ -n "$init_failure" ]]; then
            echo -e "\nError: Solr initialization failure detected:\n$init_failure" >&2
            return 1
        fi

        # Extract current, numDocs, and maxDoc values
        current=$(echo "$result" | jq '.status.collection1.index.current')
        numDocs=$(echo "$result" | jq '.status.collection1.index.numDocs')
        maxDoc=$(echo "$result" | jq '.status.collection1.index.maxDoc')

        # Display progress on the same line
        printf "\rIndexing progress: numDocs=%s, maxDoc=%s" "$numDocs" "$maxDoc"

        # Check if indexing is current
        if [[ "$current" == "true" ]]; then
            echo -e "\nIndexing complete."
            break
        fi
        sleep 1
    done
}

# 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
}

reindex_solr() {
    # Call Solr for status
    status_solr
    sudo -u dataverse curl -X DELETE http://localhost:8080/api/admin/index/timestamps || return 1
    sudo -u dataverse curl http://localhost:8080/api/admin/index/continue || return 1
    sudo -u dataverse curl http://localhost:8080/api/admin/index/status || return 1
    echo " - Waiting for solr to complete it's reindex"
    status_solr
}

set_rate_limit() {
    # Define the JSON file and the API endpoint
    API_ENDPOINT="http://localhost:8080/api/admin/settings/:RateLimitingCapacityByTierAndAction"

    # Ensure the JSON file exists
    if [[ ! -f "$RATE_LIMIT_JSON_FILE" ]]; then
        printf " - No JSON file %s not found.\n" "$RATE_LIMIT_JSON_FILE" >&2
        printf " - For more info: https://guides.dataverse.org/en/6.2/installation/config.html#rate-limiting\n"
    else
        # Use curl to send the contents of the JSON file with a PUT request
        curl "$API_ENDPOINT" -X PUT -d @"$RATE_LIMIT_JSON_FILE" -H "Content-Type: application/json" | jq || return 1
        printf " - Request sent using JSON file: %s\n" "$RATE_LIMIT_JSON_FILE"
    fi
}

update_set_permalink() {
    # Switch type from FAKE to datacite
    # https://guides.dataverse.org/en/6.2/installation/config.html#dataverse-pid-type
    local commands=(
        '-Ddataverse.pid.perma1.type=FAKE'
        '-Ddataverse.pid.perma1.label=PermaLink'
        '-Ddataverse.pid.perma1.authority=10.7281'
        '-Ddataverse.pid.perma1.shoulder=T1'
        '-Ddataverse.pid.perma1.permalink.base-url=https\://dataverse-clone.mse.jhu.edu'
        '-Ddataverse.pid.perma1.permalink.separator=\/'
        '-Ddataverse.pid.perma1.permalink.identifier-generation-style=randomString'
        '-Ddataverse.pid.default-provider=perma1'
        '-Ddataverse.pid.providers=perma1'
    )

    local cmd
    if ! sudo -u dataverse /usr/local/payara/bin/asadmin list-jvm-options | grep -F "Ddataverse.pid.providers=perma1"; then
        for cmd in "${commands[@]}"; do
                if ! sudo -u dataverse /usr/local/payara/bin/asadmin create-jvm-options "$cmd"; then
                    printf "Error: Command failed -> %s\n" "$cmd" >&2
                    return 1
                fi
        done
        printf "All commands executed successfully.\n"
    else
        printf "Permalinks already set, nothing to do.\n"
    fi
}

replace_doi_with_DOI() {
    local file="/usr/local/payara6/glassfish/domains/domain1/applications/dataverse-6.2/dataset.xhtml"
    local target_line=595

    # Ensure the file exists
    if [[ ! -f "$file" ]]; then
        printf "Error: File %s not found.\n" "$file" >&2
        return 1
    fi

    # Replace 'doi' with 'DOI' only on line 595 using sed
    sudo sed -i "${target_line}s/DatasetPage\.doi/DatasetPage\.DOI/" "$file"

    # Verify if the replacement was successful
    if ! grep -q 'DatasetPage\.DOI' "$file"; then
        printf "Error: Replacement failed.\n" >&2
        return 1
    fi

    printf "Replacement successful in file: %s\n" "$file"
}


main() {
    echo "Pre-req: ensure Payara environment variables are set"
    export PAYARA="$PAYARA"
    echo "Checking $BASHRC_FILE for payara export"
    sleep 2
    if ! sudo -u dataverse grep -qF "$PAYARA_EXPORT_LINE" "$BASHRC_FILE"; then
        printf " - Line not found in .bashrc. Adding it...\n"
        sudo bash -c "echo -e '\n$PAYARA_EXPORT_LINE' >> $BASHRC_FILE"
        printf " - Line added to .bashrc.\n"
    else
        printf " - Line already exists in .bashrc. Skipping addition.\n"
    fi

    echo -e "\nCheck if Dataverse is running the correct version"
    sleep 2
    if ! check_current_version; then
        printf " - Failed to find $CURRENT_VERSION deployed.\n" >&2
        exit 1
    fi

    echo -e "\nStep 1: Update Solr schema.xml"
    printf " - Stopping Solr.\n"
    if ! stop_solr; then
        printf " - Step 1: Error stopping Solr.\n" >&2
        exit 1
    fi

    sleep 2
    echo -e " - Downloading the Solr schema files"
    if ! download_solr_schema_file; then
        printf " - Step 1: Failed to download Solr's schema. Exiting script.\n" >&2
        exit 1
    fi
    echo -e " - Updating the Solr schema files"
    if ! update_solr_schema_file; then
        printf " - Step 1: Failed to copy Solr's schema to solr. Exiting script.\n" >&2
        exit 1
    fi

    sleep 2
    printf " - Starting Solr.\n"
    if ! start_solr; then
        printf " - Step 1: Error starting Solr.\n" >&2
        exit 1
    fi

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

    echo -e "\nStep 3: Stop Payara and clean directories"
    sleep 2
    if ! stop_payara || ! clean_generated_dir; then
        printf " - Step 3: Error stopping Payara or cleaning generated directories.\n" >&2
        exit 1
    fi

    echo -e "\nStep 4: Start Payara and deploy the new version"
    sleep 2
    if ! start_payara; then
        printf " - Step 4: Error starting Payara.\n" >&2
        exit 1
    fi

    echo -e "\nStep 5: Download WAR file."
    sleep 2
    if ! download_war_file; then
        printf " - Step 5: Failed to download WAR file. Exiting script.\n" >&2
        exit 1
    fi
    echo -e "\nStep 5: Deploying WAR file."
    if ! deploy_new_version; then
        printf " - Step 5: Error deploying new version.\n" >&2
        exit 1
    fi

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

    echo -e "\nStep 6:For installations with internationalization: Please remember to update translations via Dataverse language packs."
    echo -e " - Step 6: Skipped"
    # File are automatically pulled into /usr/local/payara6/glassfish/domains/domain1/applications/dataverse-6.2/WEB-INF/classes/propertyFiles/
    
    echo -e "\nStep 7: Restart Payara"
    sleep 2
    if ! stop_payara || ! start_payara; then
        printf " - Step 7: Error restarting Payara after deployment.\n" >&2
        exit 1
    fi

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

    echo -e "\nStep 8: Update the following Metadata Blocks to reflect the incremental improvements made to the handling of core metadata fields:"
    echo -e "Step 8: Update Geospatial Metadata Block"
    sleep 2
    if ! download_geospatial_file; then
        printf " - Step 8: Failed to download geospatial file. Exiting script.\n" >&2
        exit 1
    fi
    if ! update_geospatial_metadata_block; then
        printf " - Step 8: Failed to update geospatial metadata block. Exiting script.\n" >&2
        exit 1
    fi

    echo -e "\nStep 8: Update Citation Metadata Block"
    sleep 2
    if ! download_citation_file; then
        printf " - Step 8: Failed to download citation file. Exiting script.\n" >&2
        exit 1
    fi
    if ! update_citation_metadata_block; then
        printf " - Step 8: Failed to update citation metadata block. Exiting script.\n" >&2
        exit 1
    fi

    echo -e "\nStep 8: Update atrophysics Metadata Block"
    sleep 2
    if ! download_astrophysics_file; then
        printf " - Step 8: Failed to download atrophysics file. Exiting script.\n" >&2
        exit 1
    fi
    if ! update_astrophysics_metadata_block; then
        printf " - Step 8: Failed to update atrophysics metadata block. Exiting script.\n" >&2
        exit 1
    fi

    echo -e "\nStep 8: Update biomedical Metadata Block"
    sleep 2
    if ! download_biomedical_file; then
        printf " - Step 8: Failed to download biomedical file. Exiting script.\n" >&2
        exit 1
    fi
    if ! update_biomedical_metadata_block; then
        printf " - Step 8: Failed to update biomedical metadata block. Exiting script.\n" >&2
        exit 1
    fi

    echo -e "\nStep 8: Run ReExportAll to update dataset metadata exports."
    sleep 2
    if ! export_all_metadata; then
        printf " - Step 8: Error exporting all metadata.\n" >&2
        exit 1
    fi

    echo -e "\nStep 9: For installations with custom or experimental metadata blocks:"
    if ! stop_solr; then
        printf " - Step 9: Error stopping Solr.\n" >&2
        exit 1
    fi

    sleep 2
    if ! download_solr_schema_updater; then
        printf " - Step 9: Failed to download Solr's schema. Exiting script.\n" >&2
        exit 1
    fi
    if ! update_solr_schema_updater; then
        printf " - Step 9: Failed to update Solr schema. Exiting script.\n" >&2
        exit 1
    fi

    sleep 2
    printf " - Starting Solr.\n"
    if ! start_solr; then
        printf " - Step 9: Error starting Solr.\n" >&2
        exit 1
    fi

    echo -e "\n\nStep 9: Run Solr's reindex."
    if ! reindex_solr; then
        printf " - Step 8: Error reindexing solr.\n" >&2
        exit 1
    fi
    
    echo -e "\nAdditional Step: set rate limits."
    if ! set_rate_limit; then
        printf " - Additional Step: Error setting rate limits.\n" >&2
        exit 1
    fi
    
    echo -e "Additional Step: set permalink."
    if ! update_set_permalink; then
        printf " - Additional Step: Error setting permlink configs.\n" >&2
        exit 1
    fi

    echo -e "Additional Step: Fix when MDC is displayed"
    if ! replace_doi_with_DOI; then
        printf " - Additional Step: Error Fix when MDC is displayed #10463.\n" >&2
        printf " - IQSS/10462 - https://github.com/IQSS/dataverse/issues/10907" >&2
        exit 1
    fi

    echo -e "Additional Step: Restart Payara"
    sleep 2
    if ! stop_payara || ! start_payara; then
        printf " - Step 7: Error restarting Payara after deployment.\n" >&2
        exit 1
    fi

    sleep 2
    printf "\n\nUpgrade to Dataverse %s completed successfully.\n\n" "$TARGET_VERSION"
}

# Run the main function
main "$@"