# Setting up Local Development Database

## Introduction

You need to setup a quick local database for development without needing root permissions and polluting your environment.

* ${HOME} is the path to your home directory
* An assumption is made that the GeneNetwork2 profile is in ${HOME}/opt/gn_profiles/gn2_latest for the purposes of this documentation. Please replace as appropriate.
* We install the database files under ${HOME}/genenetwork/mariadb. Change as appropriate.

## Setup Database Server

Setup directories

```
mkdir -pv ${HOME}/genenetwork/mariadb/var/run
mkdir -pv ${HOME}/genenetwork/mariadb/var/lib/data
mkdir -pv ${HOME}/genenetwork/mariadb/var/lib/mysql
```

Setup default my.cnf

```
cat <<EOF > ${HOME}/genenetwork/mariadb/my.cnf
[client-server]
socket=${HOME}/genenetwork/mariadb/var/run/mysqld/mysqld.sock
port=3307

[server]
user=$(whoami)
socket=${HOME}/genenetwork/mariadb/var/run/mysqld/mysqld.sock
basedir=${HOME}/opt/gn_profiles/gn2_latest
datadir=${HOME}/genenetwork/mariadb/var/lib/data
ft_min_word_len=3
EOF
```

Install the database

```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysql_install_db \
    --defaults-file=${HOME}/genenetwork/mariadb/my.cnf
```

Running the daemon:

```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysqld_safe \
    --defaults-file=${HOME}/genenetwork/mariadb/my.cnf
```

Connect to daemon

```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=${HOME}/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

```
$ ${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=${HOME}/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, setup 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:

```
/home/frederick/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=/home/frederick/genenetwork/mariadb/my.cnf \
    --user=webqtlout --host=localhost --password webqtlout
```

and enter the password you provided.


## Setting up the Small Database

Download the database from

=> http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk

Say you downloaded the file in ${HOME}/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 ${HOME}/genenetwork/mariadb/var/lib/data
$ p7zip -k -d ${HOME}/Downloads/db_webqtl_s.7z
```

Now restart the server:

```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysqld_safe \
    --defaults-file=${HOME}/genenetwork/mariadb/my.cnf
```

Then update the databases

```
$ /home/frederick/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \
    --defaults-file=/home/frederick/genenetwork/mariadb/my.cnf \
    --user=frederick --password --force
```

and login as the administrative user:

```
$ /home/frederick/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=/home/frederick/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

```
/home/frederick/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=/home/frederick/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.