Getting started
Source code
Clone the Githhub repository, either through the command line
git client with:
git clone git@github.com:appliedbinf/c19r-app.git
cd c19r-appOr by creating a new project in Rstudio with: New Project > Version Control -> Git, and provide the Github repository URL above
Setup your environment (optional but recommended)
covid19RiskPlanner adopts the 12 Factor Application design philosophy,
and configuration is done via environment variables. See below for the
complete list of environment variables. Before we begin development, a
MySQL database should be setup (see deployment
vignette for MySQL setup)
Environment variables
MYSQL_USERNAME: MySQL username Note: if
MYSQL_USERNAME is empty or not set, “root” will be used
MYSQL_PASSWORD: MySQL password Note: If
MYSQL_PASSWORD is empty or not set, no password will be
used MYSQL_HOST: MySQL hostname Note: If
MYSQL_HOST is empty or not set, “localhost” wlll be
used
C19R_CASES_DIR: Optional. Alternative path to NYT
COVID19 case data. Path should not be relative.
C19R_RISK_DATA_US: Optional. Alternative path to
pre-computed risk data Path should not be relative.
C19R_RISK_DATA_EU: Optional. Alternative path to
pre-computed risk data. Path should not be relative.
C19R_EXTERNAL_UPDATES: Optional. When one of “true”,
“TRUE”, or “1” prevents app from updating NYT case data
Testing changes
After making changes to the codebase, test your changes locally using:
golem::run_dev()