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Update docker images to modify mysql configuration

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Dockerfiles are updated with two key changes:
- use streamline's official images as a base
- replace two files related to mysql configuration

A README.md file is added to the docker folder which details the changes, but
the key difference is to limit binary logs to only the `streamline` database.
This prevents additional system databases from being included, which the
database sync tools do not (yet) support.

An unrelated bugfix corrects the docker-compose image tag, specifying 'latest'
instead of a previously hard-coded version.
This commit is contained in:
alec.turner
2024-03-10 14:51:17 -07:00
parent e88aef18f4
commit 63ba4d29c8
7 changed files with 165 additions and 4 deletions
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docker/Dockerfile.streamline-emr.amd64
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FROM conrad96/streamline:2.0
FROM streamlinehealth/streamline:signalytic
COPY my.cnf /etc/mysql/my.cnf
COPY mysql-init.sh /var/www/html/.docker/mysql/mysql-init.sh
docker/Dockerfile.streamline-emr.arm64
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FROM conrad96/streamline:2.0
FROM streamlinehealth/streamline:signalytic
COPY my.cnf /etc/mysql/my.cnf
COPY mysql-init.sh /var/www/html/.docker/mysql/mysql-init.sh
docker/README.md
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# Image Notes
The base images used have a few issues that should be addressed, specifically:
- quite a few files seem to be unused, taking up space unnecessarily and making it difficult to follow
- services should ideally be run in separate docker containers - this looks to have been at least partially implemented, but is not currently used
- mysql configuration is managed in several places, in particular with respect to binary logging
- binary logging needs to be configured slightly differently to work reliably with Signalytic tools (in their current state)
A minimal set of changes has been made to the images in order to implement an initial prototype system, this includes:
- modify `/etc/mysql/my.cnf`
- limit binary logging to the `streamline` database only (`binlog-do-db=streamline`)
- remove binary log size limit (`max_binlog_size`)
- modify `/var/www/html/.docker/mysql/mysql-init.sh`
- remove binary log configuration from `mysqld` commands, using `my.cnf` as the sole configuration source (`--log-basename=bin --log-bin=/var/lib/mysql/logs/bin`)
The reason for these changes is that the Signalytic database sync tools currently work with only a single database at a time. When using MariaDB, several system databases are generated automatically, generating additional binary logs that we are not interested in. When attempting to later apply the binary logs to a database server, conflicts may arise. An alternative approach would be to drop all databases instead, this is worth investigating in the future.
docker/my.cnf
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[mysqld]
log-basename=bin
log-bin=/var/lib/mysql/logs/bin
binlog-do-db=streamline
docker/mysql-init.sh
Executable
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#!/bin/sh
# This script helps to initialise MariaDB and setup fresh database instance
# execute any pre-init scripts
for i in /scripts/pre-init.d/*sh
do
if [ -e "${i}" ]; then
echo "[i] pre-init.d - processing $i"
. "${i}"
fi
done
# create bin-logs folder
if [ ! -d "/var/lib/mysql/logs" ]; then
echo "[i] created logs folder."
mkdir -p /var/lib/mysql/logs/
fi
if [ -d "/run/mysqld" ]; then
echo "[i] mysqld already present, skipping creation"
chown -R mysql:mysql /run/mysqld
else
echo "[i] mysqld not found, creating...."
mkdir -p /run/mysqld
chown -R mysql:mysql /run/mysqld
fi
if [ -d /var/lib/mysql/mysql ]; then
echo "[i] MySQL directory already present, skipping creation"
chown -R mysql:mysql /var/lib/mysql
else
echo "[i] MySQL data directory not found, creating initial DBs"
chown -R mysql:mysql /var/lib/mysql
mysql_install_db --user=mysql --data=/var/lib/mysql > /dev/null
tfile=`mktemp`
if [ ! -f "$tfile" ]; then
return 1
fi
cat << EOF > $tfile
USE mysql;
FLUSH PRIVILEGES ;
GRANT ALL ON *.* TO 'root'@'%' identified by '$MYSQL_ROOT_PASSWORD' WITH GRANT OPTION ;
GRANT ALL ON *.* TO 'root'@'localhost' identified by '$MYSQL_ROOT_PASSWORD' WITH GRANT OPTION ;
SET PASSWORD FOR 'root'@'localhost'=PASSWORD('${MYSQL_ROOT_PASSWORD}') ;
DROP DATABASE IF EXISTS test ;
FLUSH PRIVILEGES ;
EOF
if [[ "$MYSQL_DATABASE" != "" ]]; then
echo "[i] Creating database: $MYSQL_DATABASE"
if [ "$MYSQL_CHARSET" != "" ] && [ "$MYSQL_COLLATION" != "" ]; then
echo "[i] with character set [$MYSQL_CHARSET] and collation [$MYSQL_COLLATION]"
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` CHARACTER SET $MYSQL_CHARSET COLLATE $MYSQL_COLLATION;" >> $tfile
else
echo "[i] with character set: 'utf8' and collation: 'utf8_general_ci'"
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` CHARACTER SET utf8 COLLATE utf8_general_ci;" >> $tfile
fi
if [ "$MYSQL_USER" != "" ]; then
echo "[i] Creating user: $MYSQL_USER with password $MYSQL_PASSWORD"
echo "GRANT ALL ON `$MYSQL_DATABASE`.* TO '$MYSQL_USER'@'127.0.0.1' IDENTIFIED BY '$MYSQL_PASSWORD';" >> $tfile;
echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* to '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD';" >> $tfile
fi
fi
/usr/bin/mysqld --user=mysql --bootstrap --verbose=0 --skip-name-resolve --skip-networking=0 < $tfile
# /usr/bin/mysqld --user=mysql --bootstrap --verbose=0 --skip-name-resolve --skip-networking=0 --log-basename=bin --log-bin=/var/lib/mysql/logs/bin < $tfile
rm -f $tfile
# only run if we have a starting MYSQL_DATABASE env variable AND
# the /docker-entrypoint-initdb.d/ file is not empty
if [ "$MYSQL_DATABASE" != "" ] && [ "$(ls -A /docker-entrypoint-initdb.d 2>/dev/null)" ]; then
# start the server temporarily so that we can import seed files
echo
echo "Preparing to process the contents of /docker-entrypoint-initdb.d/"
echo
TEMP_OUTPUT_LOG=/tmp/mysqld_output
/usr/bin/mysqld --user=mysql --skip-name-resolve --skip-networking=0 --silent-startup > "${TEMP_OUTPUT_LOG}" 2>&1 &
# /usr/bin/mysqld --user=mysql --skip-name-resolve --skip-networking=0 --log-basename=bin --log-bin=/var/lib/mysql/logs/bin --silent-startup > "${TEMP_OUTPUT_LOG}" 2>&1 &
PID="$!"
# watch the output log until the server is running
until tail "${TEMP_OUTPUT_LOG}" | grep -q "Version:"; do
sleep 0.2
done
# use mysql client to import seed files while temp db is running
# use the starting MYSQL_DATABASE so mysql knows where to import
MYSQL_CLIENT="/usr/bin/mysql -u root -p$MYSQL_ROOT_PASSWORD"
# loop through all the files in the seed directory
# redirect input (<) from .sql files into the mysql client command line
# pipe (|) the output of using `gunzip -c` on .sql.gz files
for f in /docker-entrypoint-initdb.d/*; do
case "$f" in
*.sql) echo " $0: running $f"; eval "${MYSQL_CLIENT} ${MYSQL_DATABASE} < $f"; echo ;;
*.sql.gz) echo " $0: running $f"; gunzip -c "$f" | eval "${MYSQL_CLIENT} ${MYSQL_DATABASE}"; echo ;;
esac
done
# send the temporary mysqld server a shutdown signal
# and wait till it's done before completeing the init process
kill -s TERM "${PID}"
wait "${PID}"
rm -f TEMP_OUTPUT_LOG
echo "Completed processing seed files."
fi;
echo
echo 'MySQL init process done. Ready for start up.'
echo
echo "exec /usr/bin/mysqld --user=mysql --console --skip-name-resolve --skip-networking=0" "$@"
# echo "exec /usr/bin/mysqld --user=mysql --console --skip-name-resolve --skip-networking=0 --log-basename=bin --log-bin=/var/lib/mysql/logs/bin " "$@"
fi
# execute any pre-exec scripts
for i in /scripts/pre-exec.d/*sh
do
if [ -e "${i}" ]; then
echo "[i] pre-exec.d - processing $i"
. ${i}
fi
done
exec /usr/bin/mysqld --user=mysql --console --skip-name-resolve --skip-networking=0 &
return $?