The goal of easydb is to simplify the process of connecting to databases using R
Install from CRAN
install.packages('easydb')
You can install the development version of easydb like so:
# install.packages('remotes')
remotes::install_github('selkamand/easydb')
library(easydb)
# Initialise a config file at '~/.easydb'
easydb_init(config_file = '~/.easydb')
# sqlite
sqlitedb <- system.file(package="easydb", "testdbs/mtcars.sqlite")
sqlite_connection <- easydb_connect(sqlitedb, config_file = '~/.easydb')
# mysql
# Example: connect to the public rfam mysql database
#
# See here for connection configuration:
# https://docs.rfam.org/en/latest/database.html
rfam_connection <- easydb_connect(dbname = "Rfam", config_file = '~/.easydb')
# postgresql
# Example: Connect to public RNAcentral postgres database
#
# See here for connection configuration:
# https://rnacentral.org/help/public-database
rna_central_connection <- easydb_connect(dbname = 'pfmegrnargs', config_file = '~/.easydb')
# Don't forget to disconnect from databases when you finish!
easydb_disconnect(sqlite_connection)
easydb_disconnect(rna_central_connection)
easydb_disconnect(rfam_connection)
Once you’ve finished working with a database, its best to disconnect
from the db using easydb_disconnect(connection_object)
We need to store your configuration details in a file somewhere on disk. You can choose where.
A common practice is to create a hidden file in your home directory.
We’ll create our config file: ~/.easydb
easydb_init(config_file = '~/.easydb')
This only needs to be done once.
Connect to databases:
easydb_connect('database_name', '~/.easydb')
Disconnect from databases:
easydb_disconnect(connection)
The first time you try to connect to a database, you may have to answer some questions about the database (depending on the database type you’re connecting to).
Once you’ve setup the configuration, you will not have to re-enter
host/port/creds unless you set the argument from_scratch = TRUE
. This
argument will delete the existing configuration and credentials for the
given database and prompt you to supply updated information.
# List previously configured databases
easydb_available_databases('~/.easydb')
Database configurations (host, port, driver, etc) are stored in a
configuration file that will be created at a user-specified location (we
recommend ~/.easydb
).
Credentials are stored separately in your operating systems credential
store. This is powered by keyring
. If you’re on linux you may need to
install the secret service library. See the
readme for details