docker-entrypoint.sh

#!/bin/bash
set -e

mkdir -p /var/run/mysqld
chmod -R 777 /var/run/mysqld

# if command starts with an option, prepend mysqld
if [ "${1:0:1}" = '-' ]; then
	set -- mysqld "$@"
fi

if [ "$1" = 'mysqld' ]; then
	# Test we're able to startup without errors. We redirect stdout to /dev/null so
	# only the error messages are left.
	result=0
	output=$("$@" --verbose --help 2>&1 > /dev/null) || result=$?
	if [ ! "$result" = "0" ]; then
		echo >&2 'error: could not run mysql. This could be caused by a misconfigured my.cnf'
		echo >&2 "$output"
		exit 1
	fi

	# Get config
	DATADIR="$("$@" --verbose --help 2>/dev/null | awk '$1 == "datadir" { print $2; exit }')"

	if [ ! -d "$DATADIR/mysql" ]; then
		if [ -z "$MYSQL_ROOT_PASSWORD" -a -z "$MYSQL_ALLOW_EMPTY_PASSWORD" -a -z "$MYSQL_RANDOM_ROOT_PASSWORD" ]; then
			echo >&2 'error: database is uninitialized and password option is not specified '
			echo >&2 '  You need to specify one of MYSQL_ROOT_PASSWORD, MYSQL_ALLOW_EMPTY_PASSWORD and MYSQL_RANDOM_ROOT_PASSWORD'
			exit 1
		fi
		# If the password variable is a filename we use the contents of the file
		if [ -f "$MYSQL_ROOT_PASSWORD" ]; then
			MYSQL_ROOT_PASSWORD="$(cat $MYSQL_ROOT_PASSWORD)"
		fi
		mkdir -p "$DATADIR"
		chown -R mysql:mysql "$DATADIR"

		echo 'Running mysql_install_db'
		mysql_install_db --user=mysql --datadir="$DATADIR" --rpm
		echo 'Finished mysql_install_db'

		"$@" --skip-networking &
		pid="$!"

		mysql=( mysql --protocol=socket -uroot )

		for i in {30..0}; do
			if echo 'SELECT 1' | "${mysql[@]}" &> /dev/null; then
				break
			fi
			echo 'MySQL init process in progress...'
			sleep 1
		done
		if [ "$i" = 0 ]; then
			echo >&2 'MySQL init process failed.'
			exit 1
		fi

		mysql_tzinfo_to_sql /usr/share/zoneinfo | "${mysql[@]}" mysql

		if [ ! -z "$MYSQL_RANDOM_ROOT_PASSWORD" ]; then
			MYSQL_ROOT_PASSWORD="$(pwmake 128)"
			echo "GENERATED ROOT PASSWORD: $MYSQL_ROOT_PASSWORD"
		fi
		"${mysql[@]}" <<-EOSQL
			-- What's done in this file shouldn't be replicated
			--  or products like mysql-fabric won't work
			SET @@SESSION.SQL_LOG_BIN=0;
			DELETE FROM mysql.user ;
			CREATE USER 'root'@'%' IDENTIFIED BY '${MYSQL_ROOT_PASSWORD}' ;
			GRANT ALL ON *.* TO 'root'@'%' WITH GRANT OPTION ;
			DROP DATABASE IF EXISTS test ;
			FLUSH PRIVILEGES ;


		EOSQL
		if [ ! -z "$MYSQL_ROOT_PASSWORD" ]; then
			mysql+=( -p"${MYSQL_ROOT_PASSWORD}" )
		fi

		if [ "$MYSQL_DATABASE" ]; then
			echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" | "${mysql[@]}"
			mysql+=( "$MYSQL_DATABASE" )
		fi

		if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then
			echo "CREATE USER '"$MYSQL_USER"'@'%' IDENTIFIED BY '"$MYSQL_PASSWORD"' ;" | "${mysql[@]}"

			if [ "$MYSQL_DATABASE" ]; then
				echo "GRANT ALL ON \`"$MYSQL_DATABASE"\`.* TO '"$MYSQL_USER"'@'%' ;" | "${mysql[@]}"
			fi

			echo 'FLUSH PRIVILEGES ;' | "${mysql[@]}"


			echo "use $MYSQL_DATABASE;
				CREATE TABLE `gskb` (
			  `label` varchar(255) NOT NULL,
			  `species` varchar(255) NOT NULL,
			  `source` varchar(255) NOT NULL,
			  `regType` enum('different','down','up') DEFAULT NULL,
			  `chip` varchar(255) DEFAULT NULL,
			  `detailsUrl` text,
			  `nGenes` smallint(4) unsigned NOT NULL,
			  `descriptionBrief` text NOT NULL,
			  `descriptionFull` text,
			  `pubmed` varchar(20) DEFAULT NULL,
			  `firstAuthor` varchar(255) DEFAULT NULL,
			  `paperTitle` text,
			  `year` decimal(4,0) DEFAULT NULL,
			  `citation` tinytext,
			  `comment` tinytext,
			  `genes` mediumtext NOT NULL,
			  `genesSym` mediumtext NOT NULL,
			  PRIMARY KEY (`label`),
			  KEY `gskb_species_idx` (`species`),
			  KEY `gskb_source_idx` (`source`),
			  FULLTEXT KEY `gskb_fulltext_idx` (`label`,`firstAuthor`,`descriptionBrief`,`genes`,`genesSym`,`citation`),
			  FULLTEXT KEY `gskb_genesym_fulltext_idx` (`genesSym`)
			) ENGINE=MyISAM DEFAULT CHARSET=utf8 PACK_KEYS=1 ;
			"
		fi

		echo
		for f in /docker-entrypoint-initdb.d/*; do
			case "$f" in
				*.sh)  echo "$0: running $f"; . "$f" ;;
				*.sql) echo "$0: running $f"; "${mysql[@]}" < "$f" && echo ;;
				*)     echo "$0: ignoring $f" ;;
			esac
			echo
		done

		if ! kill -s TERM "$pid" || ! wait "$pid"; then
			echo >&2 'MySQL init process failed.'
			exit 1
		fi

		echo
		echo 'MySQL init process done. Ready for start up.'
		echo
	fi

	chown -R mysql:mysql "$DATADIR"
fi

exec "$@"