diff options
| -rwxr-xr-x | genenetwork-local-container.sh | 89 |
1 files changed, 89 insertions, 0 deletions
diff --git a/genenetwork-local-container.sh b/genenetwork-local-container.sh index 8e599e4..2bbe529 100755 --- a/genenetwork-local-container.sh +++ b/genenetwork-local-container.sh @@ -261,3 +261,92 @@ if [ "$1" = "--init-container" ]; then log "INFO" "Email: test@development.user" log "INFO" "Password: testpasswd" fi + +if [ "$1" = "--init-sql" ]; then + # Configuration + URL="https://files.genenetwork.org/database/db_webqtl_s-2025-02-18.sql.xz" + DOWNLOAD_DIR="/tmp" + FILE_NAME=$(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 + + # 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 + + # Extract the .xz file + 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 + + # 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" + exit 0 +fi |