diff options
| -rw-r--r-- | topics/setting-up-local-development-database.gmi | 69 |
1 files changed, 34 insertions, 35 deletions
diff --git a/topics/setting-up-local-development-database.gmi b/topics/setting-up-local-development-database.gmi index 67dd88d..1f844c3 100644 --- a/topics/setting-up-local-development-database.gmi +++ b/topics/setting-up-local-development-database.gmi @@ -4,33 +4,32 @@ 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. +* An assumption is made that the GeneNetwork2 profile is in ~/opt/gn_profiles/gn2_latest for the purposes of this documentation. Please replace as appropriate. +* We install the database files under ~/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 +mkdir -pv ~/genenetwork/mariadb/var/run +mkdir -pv ~/genenetwork/mariadb/var/lib/data +mkdir -pv ~/genenetwork/mariadb/var/lib/mysql ``` Setup default my.cnf ``` -cat <<EOF > ${HOME}/genenetwork/mariadb/my.cnf +cat <<EOF > ~/genenetwork/mariadb/my.cnf [client-server] -socket=${HOME}/genenetwork/mariadb/var/run/mysqld/mysqld.sock +socket=~/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 +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 ``` @@ -38,22 +37,22 @@ EOF Install the database ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysql_install_db \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf +~/opt/gn_profiles/gn2_latest/bin/mysql_install_db \ + --defaults-file=~/genenetwork/mariadb/my.cnf ``` Running the daemon: ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysqld_safe \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf +~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \ + --defaults-file=~/genenetwork/mariadb/my.cnf ``` Connect to daemon ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf +~/opt/gn_profiles/gn2_latest/bin/mysql \ + --defaults-file=~/genenetwork/mariadb/my.cnf ``` Set up password for user @@ -67,8 +66,8 @@ 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 +$ ~/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. @@ -84,8 +83,8 @@ 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 \ +~/opt/gn_profiles/gn2_latest/bin/mysql \ + --defaults-file=~/genenetwork/mariadb/my.cnf \ --user=webqtlout --host=localhost --password webqtlout ``` @@ -98,7 +97,7 @@ 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. +Say you downloaded the file in ~/Downloads, you can now add the database to your server. First stop the server: @@ -110,30 +109,30 @@ $ 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 ${HOME}/Downloads/db_webqtl_s.7z +$ cd ~/genenetwork/mariadb/var/lib/data +$ p7zip -k -d ~/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 +~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \ + --defaults-file=~/genenetwork/mariadb/my.cnf ``` Then update the databases ``` -$ ${HOME}/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf \ +$ ~/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \ + --defaults-file=~/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 \ +$ ~/opt/gn_profiles/gn2_latest/bin/mysql \ + --defaults-file=~/genenetwork/mariadb/my.cnf \ --user=$(whoami) --password ``` @@ -146,8 +145,8 @@ MariaDB [mysql]> GRANT ALL PRIVILEGES ON db_webqtl_s.* TO 'webqtlout'@'localhost now logout as the administrative user and log back in as the normal user ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf \ +~/opt/gn_profiles/gn2_latest/bin/mysql \ + --defaults-file=~/genenetwork/mariadb/my.cnf \ --user=webqtlout --host=localhost --password db_webqtlout_s MariaDB [db_webqtlout_s]> SELECT * FROM ProbeSetData LIMIT 20; @@ -160,8 +159,8 @@ verify you see some data. So far, we have been connecting to the server by specifying --defaults-file option, e.g. ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \ - --defaults-file=${HOME}/genenetwork/mariadb/my.cnf \ +~/opt/gn_profiles/gn2_latest/bin/mysql \ + --defaults-file=~/genenetwork/mariadb/my.cnf \ --user=webqtlout --host=localhost --password db_webqtlout_s ``` @@ -170,7 +169,7 @@ which allows connection via the unix socket. We could drop that specification and connect via the port with: ``` -${HOME}/opt/gn_profiles/gn2_latest/bin/mysql \ +~/opt/gn_profiles/gn2_latest/bin/mysql \ --user=webqtlout --host=127.0.0.1 --port=3307 --password db_webqtlout_s ``` |