agrotoxinDB

An R API to the agroToxin database using R6 objects.

Usage:

library(agrotoxinDB)

dbc <- DBConnection$new(host = "localhost", user = "anonymous", password = "")
compound.handle <- CompoundHandle$new(dbc)
compounds <- compound.handle$get_all_compounds()

How to recreate the database locally

The instructions below are for Debian-based Linux systems (e.g. Ubuntu). Note that you need admin privileges on the machine.

1. Install a MariaDB server

sudo apt update
sudo apt install mariadb-server mariadb-client -y

2. Configure the server

sudo mysql_secure_installation

This will walk you through some prompts to secure the server.
Since it should be a fresh installation, simply press ENTER at the first prompt
then N when asked to set up a root password and finally Y for all subsequent ones.

3. Set up an administrative user

sudo mariadb

Then at the MariaDB prompt:

 GRANT ALL ON *.* TO 'admin'@'localhost' IDENTIFIED BY '<password>' WITH GRANT OPTION;
 FLUSH PRIVILEGES;
 \q

4. Create the database
   Download the database dump file (agrotoxin_database.sql) from the web site to the current working directory.
   Log back in using the admin account:

mariadb -u admin -p

Enter the password you selected above then at the MariaDB prompt:

SOURCE agrotoxin_database.sql
\q

5. Set up a passwordless account for querying the database.
   Log back in using the admin account:

mariadb -u admin -p

Enter the password you selected above then at the MariaDB prompt:

CREATE USER 'anonymous'@'%';
GRANT SELECT ON `agroTox%`.* TO 'anonymous'@'%';
FLUSH PRIVILEGES;
\q