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| -rw-r--r-- | topics/setting-up-local-development-database.gmi | 66 |
1 files changed, 65 insertions, 1 deletions
diff --git a/topics/setting-up-local-development-database.gmi b/topics/setting-up-local-development-database.gmi index c2856a8..3c6c291 100644 --- a/topics/setting-up-local-development-database.gmi +++ b/topics/setting-up-local-development-database.gmi @@ -8,7 +8,7 @@ You need to setup a quick local database for development without needing root pe * 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. -## Steps +## Setup Database Server Setup directories @@ -90,3 +90,67 @@ Now logout, and log back in as the new webqtlout user: ``` 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. |