ref/Git_PAT_setup.md

In PHSKC-APDE/rads: Assisted computation of King County public health data

How to access files from a private repo in R

Problem: you need to pull a file/data from a private repo

• Imagine you want to pull in a csv file from a private repo you have access to.
• On public repos, you simply pull in the data from 'https://raw.githubusercontent.com////', usually copying the file name from your web browser.
• However, in a private repo, that URL has a suffix after the '.csv' part that looks like '?token=AEWDGFSWVNEWWF5AB8WPXKY2ZND'. This is a temporary access token that will only work in your code for a short period of time. You need a longer-lasting solution.

Solution overview: use your own personal access token

The general approach is to set up a permanent token that you will use in R, using the following broad steps: 1. Set up the token in Github. 2. Add the token to your Windows environmental variables. 3. Use the httr package to send your credentials when accessing the file.

Set up your personal access token (PAT)

1. Go to https://github.com/settings/tokens.
2. Click the button that says 'Generate new token' (you may need to enter your password).
3. In the note field, add something along the lines of 'win_env' so you know where this token will be used.
4. Under the scopes, check the 'repo' option. Everything else can be unchecked.
5. Click 'Generate token'.
6. A 40-character string will appear. This is the only time you will see the PAT so do not close your browser yet. Copy this character string.
7. If you mess things up and the PAT disappears, restart at step 1 with a new token (first, delete the token you just created after you click on the link in step 1).

Add the PAT to your Windows environmental variables

1. Hit the windows key and type "edit environment variables" in the search bar. 
2. Hit enter to open Environment Variables window
3. Click Edit... in the top half of the window (i.e., the part that has the title "User variables for xyz")
4. In the Variable name:box, type GITHUB_TOKEN
5. In the Variable value: box, paste your PAT (40-character string that you copied from github.com)
6. Click OK
7. While you're here, you might as well save the same PAT with another commonly referenced name. Repeat steps 3 through 6, but change GITHUB_TOKEN to GITHUB_PAT when you repeat step 4.
8. Click OK on the bottom right of the to close the Environment Variables window.

Use the PAT to access the private repo

First test that your PAT is working as hoped by typing the following in the R console: auth <- Sys.getenv("GITHUB_TOKEN")

Make sure that the auth object is your PAT. If not, seek assistance at R office hours or from a colleague.

You can now use the authenticate command in the httr package to pass your PAT. Here are some examples of how to access code:

get a YAML file config_file <- yaml::yaml.load(httr::GET( url = "https://raw.githubusercontent.com/PHSKC-APDE/bskhs/master/etl/load_raw/load_load_raw.bskhs_2017_phone_web.yaml", httr::authenticate(auth, "")))

run R code eval(parse(text = httr::content(httr::GET( url = "https://raw.githubusercontent.com/PHSKC-APDE/bskhs/master/etl/scripts_general/load_table_bskhs.R", httr::authenticate(auth, "")), "text")))

get a CSV bskhs_2019_names <- vroom::vroom(httr::content(httr::GET( url = "https://raw.githubusercontent.com/PHSKC-APDE/bskhs/master/etl/ref/field_names.csv", httr::authenticate(Sys.getenv("GITHUB_PAT"), "")), type = "text"))

PHSKC-APDE/rads documentation built on April 14, 2025, 10:47 a.m.