Added a Linux/Bash Backup script that can be run from CronTab

modules/util_backup/backup-full.sh

@@ -0,0 +1,240 @@
+#!/usr/bin/env bash
+#
+# Backup libreehr directory and database
+#
+# LICENSE: This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0
+# See the Mozilla Public License for more details.
+# If a copy of the MPL was not distributed with this file, You can obtain one at https://mozilla.org/MPL/2.0/.
+#
+# @package Librehealth EHR
+# @author Sam Likins <[email protected]>
+# @author Tony McCormick <[email protected]>
+# @link http://librehealth.io
+#
+# Please help the overall project by sending changes you make to the author and to the LibreEHR community.
+#
+
+if [[ $(whoami) != "root" ]]; then
+	echo "You must be root to run this script."
+	exit 1
+fi
+
+# Configure run -defaults if no arguments are passed
+LIBREEHR_PATH="${1:-/var/www/html/libreehr}"
+LIBREEHR_SITE="${2:-default}"
+ARCHIVE_PATH="${3:-/mnt/backups}"
+BACKUP_NAME="${4:-emr_backup}"
+TEMPDIR="${5:-/mnt/backups/tmp}"
+
+# Include routines during backup when de-identification is enabled
+INCLUDE_DE_IDENTIFICATION="false"
+
+
+#############
+# FUNCTIONS #
+#############
+
+function display_message {
+	echo "# $1"
+}
+
+function display_exit {
+	local MESSAGE="$1"
+	local EXIT_CODE="${2:-1}"
+
+	echo "* ERROR: $MESSAGE"
+	exit "$EXIT_CODE"
+}
+
+function create_gzip {
+	local FILE="$1"
+
+	$CMD_GZIP $FILE
+
+	if [[ ! -f "$FILE.gz" ]]; then
+		display_exit "Failed to create GZip file: $FILE.gz"
+	fi
+}
+
+function create_tar_archive {
+	local ARCHIVE_NAME="$1"
+	local COMPRESS_METHOD="$2"
+	local FILES="$3"
+
+	if [[ "$COMPRESS_METHOD" == "gz" ]]; then
+		local OPTIONS="--same-owner --ignore-failed-read -zcphf";
+	else
+		local OPTIONS="-cpf";
+	fi
+
+	$CMD_TAR $OPTIONS $ARCHIVE_NAME $FILES
+
+	if [[ ! -f "$ARCHIVE_NAME" ]]; then
+		display_exit "Failed to create TAR archive file: $ARCHIVE_NAME"
+	fi
+}
+
+function get_libreehr_backup_files {
+	# Return all files and directories substituting sites for sites/$LIBREEHR_SITE and removing newlines
+	echo "$(ls -1 "$LIBREEHR_PATH" | sed -e "s|sites|sites/$LIBREEHR_SITE|g" | sed ':a;N;$!ba;s/\n/ /g')"
+}
+
+function get_sqlconf_value {
+	local VALUE=$1
+	local SOURCE="$LIBREEHR_PATH/sites/$LIBREEHR_SITE/sqlconf.php"
+
+	if [[ ! -f "$SOURCE" ]]; then
+		display_exit "Failed locating libreehr MySQL configuration file for '$LIBREEHR_SITE': $SOURCE" >&2
+	fi
+
+	$CMD_PHP -r "require '$SOURCE'; echo \$$VALUE;"
+}
+
+function create_files_backup {
+	local CPWD="$(pwd)"
+	cd "$LIBREEHR_PATH"
+
+	display_message "Generating TAR GZip archive of libreehr files"
+
+	create_tar_archive "$SITE_TAR_GZ" 'gz' "$(get_libreehr_backup_files)"
+
+	display_message "Finished generating TAR GZip"
+
+	cd "$CPWD"
+}
+
+function create_database_backup {
+	display_message "Retrieving database connection information from libreehr"
+
+	local LIBREEHR_DB_LOGIN="$(get_sqlconf_value "login")"
+	local LIBREEHR_DB_PASS="$(get_sqlconf_value "pass")"
+	local LIBREEHR_DB_HOST="$(get_sqlconf_value "host")"
+	local LIBREEHR_DB_PORT="$(get_sqlconf_value "port")"
+	local LIBREEHR_DB_DBASE="$(get_sqlconf_value "dbase")"
+
+	local OPTIONS="-u $LIBREEHR_DB_LOGIN -p$LIBREEHR_DB_PASS"
+	local OPTIONS="$OPTIONS -h$LIBREEHR_DB_HOST --port=$LIBREEHR_DB_PORT"
+	[[ "$INCLUDE_DE_IDENTIFICATION" == "true" ]] && local OPTIONS="$OPTIONS --routines"
+	local OPTIONS="$OPTIONS --opt --quote-names"
+	local OPTIONS="$OPTIONS -r $DATABASE_SQL $LIBREEHR_DB_DBASE"
+
+	display_message "Beginning database dump"
+
+	$CMD_MYSQLDUMP $OPTIONS
+
+	if [[ $? -gt 0 ]]; then
+		display_exit "MySQL dump of database '$LIBREEHR_DB_DBASE' on '$LIBREEHR_DB_HOST:$LIBREEHR_DB_PORT' with user '$LIBREEHR_DB_LOGIN' failed"
+	elif [[ ! -f "$DATABASE_SQL" ]]; then
+		display_exit "Failed to create MySQL dump file: $DATABASE_SQL"
+	fi
+
+	display_message "Finished database dump"
+
+	display_message "Placing database dump in a GunZip archive"
+
+	create_gzip "$DATABASE_SQL"
+}
+
+function create_libreehr_backup {
+	mkdir -p "$BACKUP_PATH"
+
+	display_message "Backing up libreehr files"
+	create_files_backup
+
+	display_message "Backing up libreehr database"
+	create_database_backup
+
+	display_message "Wrapping backup in TAR archive file"
+	local CPWD="$(pwd)"
+	cd "$TEMP_PATH"
+
+	create_tar_archive "$BACKUP_TAR" '' "$BACKUP_NAME"
+
+	cd "$CPWD"
+}
+
+# Define cleanup process
+function finish {
+	if [[ -d "$TEMP_PATH" ]]; then
+		display_message "Removing temporary work directory: $TEMP_PATH"
+		rm -fr -- "$TEMP_PATH"
+	fi
+}
+
+
+display_message "Initializing libreehr backup: $(date +"%F %r")"
+
+
+# Test provided paths exists
+if [[ ! -d "$LIBREEHR_PATH" ]]; then
+	display_exit "libreehr path doesn't exist: $LIBREEHR_PATH"
+elif [[ ! -d "$LIBREEHR_PATH/sites/$LIBREEHR_SITE" ]]; then
+	display_exit "libreehr site doesn't exist: $LIBREEHR_SITE"
+elif [[ ! -d "$ARCHIVE_PATH" ]]; then
+	display_exit "Archive path doesn't exist: $ARCHIVE_PATH"
+fi
+
+
+# Determine the path to the systems temporary directory
+if [[ -d "$TMPDIR" ]]; then
+	TEMP_PATH="$TMPDIR"
+elif [[ -d "$TMP" ]]; then
+	TEMP_PATH="$TMP"
+elif [[ -d /var/tmp ]]; then
+	TEMP_PATH=/var/tmp
+elif [[ -d /tmp ]]; then
+	TEMP_PATH=/tmp
+else
+	TEMP_PATH="$(pwd)"
+fi
+
+
+################
+# START SCRIPT #
+################
+
+display_message "Established system temporary directory: $TEMP_PATH"
+
+
+# Generate a temporary directory to work in
+TEMP_PATH="$(mktemp -d --tmpdir="$TEMP_PATH" "libreehr_backup.XXXXXXXX")"
+
+display_message "Created temporary work directory: $TEMP_PATH"
+
+
+# Register trap cleanup process
+trap finish INT TERM HUP EXIT
+
+
+display_message "Determining necessary file paths and command locations"
+
+BACKUP_PATH="$TEMP_PATH/$BACKUP_NAME"
+DATABASE_SQL="$BACKUP_PATH/libreehr.sql"
+SITE_TAR_GZ="$BACKUP_PATH/libreehr.tar.gz"
+BACKUP_TAR="$BACKUP_PATH.tar"
+ARCHIVE_TAR="$ARCHIVE_PATH/$(date +"%Y/%F")-$BACKUP_NAME-$LIBREEHR_SITE.tar"
+
+CMD_GZIP="$(which gzip | head -n1)"
+CMD_TAR="$(which tar | head -n1)"
+CMD_PHP="$(which php | head -n1)"
+CMD_MYSQLDUMP="$(which mysqldump | head -n1)"
+
+
+display_message "Beginning backup of libreehr components"
+
+create_libreehr_backup
+
+
+if [[ -f "$BACKUP_TAR" ]]; then
+	if [[ ! -d "$(dirname "$ARCHIVE_TAR")" ]]; then
+		mkdir -p "$(dirname "$ARCHIVE_TAR")"
+	fi
+
+	display_message "Moving generated backup to archive location: $ARCHIVE_TAR"
+
+	mv "$BACKUP_TAR" "$ARCHIVE_TAR"
+else
+	display_exit "Missing backup tar file: $BACKUP_TAR"
+fi
+
+display_message "Finalized libreehr backup: $(date +"%F %r")"