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# 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:
```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=${HOME}/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
```
$ ${HOME}/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \
--defaults-file=${HOME}/genenetwork/mariadb/my.cnf \
--user=frederick --password --force
```
and login as the administrative user:
```
$ ${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=${HOME}/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
```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=${HOME}/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.
### A Note on Connection to the Server
So far, we have been connecting to the server by specifying --defaults-file option, e.g.
```
${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \
--defaults-file=${HOME}/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:
```
${HOME}/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.
|
