You need to set up a quick local database for development without polluting your environment.
You can use ssh tunneling to access mysql from your machine. Try something like:
ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org mysql -uwebqtlout -pwebqtlout -h 127.0.0.1 db_webqtl -A -e "show tables;"
If you already have that port in use on your machine try
ssh -L 3307:127.0.0.1:3306 -f -N tux02.genenetwork.org mysql -uwebqtlout -pwebqtlout -h 127.0.0.1 -P 3307 db_webqtl -A -e "show tables;"
To keep the connection alive add something like this to your `~/.ssh/config`
ServerAliveInterval 60 ServerAliveCountMax 10
For specific hosts you can set it up as
Host tux02 HostName tux02.genenetwork.org TCPKeepAlive yes ServerAliveInterval 60 user myname
Setting up mariadb in a Guix container is the preferred and easier method. But, you need root access to run the container. The genenetwork2 repo comes with a guix system container definition to run MariaDB and Redis. From the genenetwork2 repo, you can build and run the container using:
$ sudo $(./containers/db-container.sh)
By default, mariadb allows passwordless login for root only on the local machine. So, enter the container using guix container exec and set the root password to a blank.
$ mysql -u root
MariaDB [(none)]> SET PASSWORD = PASSWORD("");
You should now be able to connect to the database from outside the container using
$ mysql --protocol tcp -u root
Create a database db_webqtl_s
MariaDB [mysql]> CREATE DATABASE db_webqtl_s;
Load the small database dump into the database. You may find the small database either on space or tux02 at /home/aruni/gn2.sql.lz
$ lzip -cd gn2.sql.lz | mysql --protocol tcp -u root db_webqtl_s
Since this is a develpoment server accessible only from localhost, it is ok to use the root user with no password. Configure your development instance of genenetwork2 with the following SQL_URI.
SQL_URI="mysql://root@127.0.0.1:3306/db_webqtl_s"
A local container runs as a normal user. It requires some juggling of dirs to load an existing database. Make sure to not run on the same dirs as another mariadb instance(!) Here we run a new database, but you can use an existing DB as was done in
cd ~/tmp/mariadb mkdir var ~/tmp/mariadb$ ~/opt/guix-pull/bin/guix shell -C -N coreutils sed mariadb --share=var=/var --share=/export2/tmp=/tmp
inside the container
mkdir -p /var/lib/data mkdir -p /var/lib/mysql mkdir /var/run
Initialize with
mysql_install_db
and run, for example
export TMPDIR=/tmp mysqld_safe --datadir='/var/lib/mysql/' --port=3307 --user=$USER --group=users --nowatch --socket=/var/run/mysqld/mysqld.sock
Now from the container you should be able to connect with the socket
/export/mysql$ ~/opt/guix-pull/bin/guix shell mysql -- mysql --socket=var/run/mysqld/mysqld.sock -uwebqtlout -pwebqtlout db_webqtl
and
Welcome to the MariaDB monitor. Commands end with ; or \g. Your MariaDB connection id is 3 Server version: 10.5.12-MariaDB MariaDB Server Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. MariaDB [(none)]> show databases; +--------------------+ | Database | +--------------------+ | information_schema | | mysql | | performance_schema | | test | +--------------------+ 4 rows in set (0.001 sec)
To run/bind on a network interface we can open up with:
export TMPDIR=/tmp mysqld_safe --datadir='/var/lib/mysql/' --port=3307 --user=$USER --group=users --nowatch --bind-address 127.0.0.1 --socket=/var/run/mysqld/mysqld.sock
Test with
~/opt/guix-pull/bin/guix shell mysql -- mysql -uwebqtlout -pwebqtlout db_webqtl -h 127.0.0.1 --port=3307
Please don't use world writeable bind-address 0.0.0.0. If you run it for your own purposes use ssh tunneling instead (see above).
If you need to tweak the server configuration you can load the my.cnf file with the `--defaults-file=var/my.cnf` inside and outside the container.
/This is not recommended/
Set up directories
mkdir -pv ~/genenetwork/mariadb/var/run mkdir -pv ~/genenetwork/mariadb/var/lib/data mkdir -pv ~/genenetwork/mariadb/var/lib/mysql
Set up default my.cnf
cat <<EOF > ~/genenetwork/mariadb/my.cnf [client-server] socket=~/genenetwork/mariadb/var/run/mysqld/mysqld.sock port=3307 [server] user=$(whoami) socket=~/genenetwork/mariadb/var/run/mysqld/mysqld.sock basedir=~/opt/gn_profiles/gn2_latest datadir=~/genenetwork/mariadb/var/lib/data ft_min_word_len=3 EOF
Install the database
~/opt/gn_profiles/gn2_latest/bin/mysql_install_db \
--defaults-file=~/genenetwork/mariadb/my.cnf
Running the daemon:
~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \
--defaults-file=~/genenetwork/mariadb/my.cnf
Connect to daemon
~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf
Set up password for user
MariaDB [(none)]> USE mysql; MariaDB [mysql]> ALTER USER '<your-username>'@'localhost' IDENTIFIED BY '<the-new-password>'; MariaDB [mysql]> FLUSH PRIVILEGES;
Now logout and login again with
$ ~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf --password mysql
enter the newly set password and voila, you are logged in and your user has the password set up.
Now, set up a new user, say webqtlout, and a default database they can connect to
MariaDB [mysql]> CREATE DATABASE webqtlout; MariaDB [mysql]> CREATE USER 'webqtlout'@'localhost' IDENTIFIED BY '<some-password>'; MariaDB [mysql]> GRANT ALL PRIVILEGES ON webqtlout.* TO 'webqtlout'@'localhost';
Now logout, and log back in as the new webqtlout user:
~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf \
--user=webqtlout --host=localhost --password webqtlout
and enter the password you provided.
Download the database from
Say you downloaded the file in ~/Downloads, you can now add the database to your server.
First stop the server:
$ ps aux | grep mysqld # get the process ids $ kill -s SIGTERM <pid-of-mysqld> <pid-of-mysqld_safe>
Now extract the database archive in the mysql data directory:
$ cd ~/genenetwork/mariadb/var/lib/data $ p7zip -k -d ~/Downloads/db_webqtl_s.7z
Now restart the server:
~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \
--defaults-file=~/genenetwork/mariadb/my.cnf
Then update the databases
$ ~/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \
--defaults-file=~/genenetwork/mariadb/my.cnf \
--user=frederick --password --force
and login as the administrative user:
$ ~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf \
--user=$(whoami) --password
and grant the privileges to your normal user:
MariaDB [mysql]> GRANT ALL PRIVILEGES ON db_webqtl_s.* TO 'webqtlout'@'localhost';
now logout as the administrative user and log back in as the normal user
~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf \
--user=webqtlout --host=localhost --password db_webqtlout_s
MariaDB [db_webqtlout_s]> SELECT * FROM ProbeSetData LIMIT 20;
verify you see some data.
So far, we have been connecting to the server by specifying --defaults-file option, e.g.
~/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=~/genenetwork/mariadb/my.cnf \
--user=webqtlout --host=localhost --password db_webqtlout_s
which allows connection via the unix socket.
We could drop that specification and connect via the port with:
~/opt/gn_profiles/gn2_latest/bin/mysql \
--user=webqtlout --host=127.0.0.1 --port=3307 --password db_webqtlout_s
In this version, the host specification was changed from
--host=localhost
to
--host=127.0.0.1
whereas, the **--defaults-file** file specification was dropped and a new **--port** specification was added.