jonahb13 / clinical-trials-viz

ClinicalTrialsViz

Setting up system environment variables:

To access the clinical trials database, you will be prompted with a username and password to connect. Before using the files in this repository, you must do the following:

• Go to the home directory of your terminal cd $HOME

• Create a new file called .Renviron sudo nano .Renviron

• Inside the file write your username, password, and host environment variables with your database login information:

userid = "'your database account username'"
userpass = "'your database account password'"
host = "'your database endpoint'"

**Important: for our moravian college username, password, and database endpoint information reference our 1password entry under "AACT AWS Instance" notes

• Save and exit nano pressing the keys ctrl+c, ctrl+x, y, enter

• Restart your R studio application to ensure environment variables are processed

• Now you may use the scripts available in the repository, these environment variables will be referenced later using the syntax Sys.getenv()

Allowing access to AWS instance

• Connect to the AWS website and click on the RDS section

• Click on the database labeled "clinicaltrialsdatabase"

• Under the "Connectivity & security" tab, find "Security" and click on the blue link directly under "VPC security groups"

• Click on the "inbound" tab and click edit

• Click "Add Rule" and create a new Custom TCP Rule with port range 5432 and for the source drop-down menu click "My IP", then click save

• If this is done correctly, your computer will now be able to pass through security and connect to the database

Connecting to the database

• First-time startup enter the command (this command will only ever need to be entered one time) install.packages("RPostgreSQL")

• Then you must access the RPostgreSQL library to use the commands library(RPostgreSQL)

• Initialize database driver drv <- dbDriver('PostgreSQL')

• Connect to database with user environment variables

con <- dbConnect(drv,
    dbname="aact",
    host=Sys.getenv("host"),
    port=5432,
    user=Sys.getenv("userid"),
    password=Sys.getenv("userpass")
)

• Make the database schema public for easier query syntax dbExecute(con, "SET search_path TO ctgov,public")

• Test that your connection is valid with a sample database query command sample <- dbGetQuery(con, "select distinct study_type from studies")