QC for brentlab RNAseq data

getUserAuthToken

R Documentation

get (via a http POST request) your user authentication token from the database

Description

get (via a http POST request) your user authentication token from the database

Usage

getUserAuthToken(url, username, password)

Arguments

`url`	check the database_info variable. for configured organisms, you can find this under database_info$organism$token_auth
`username`	a valid username for the database. If you don't have one, then you'll need to ask for one to be created
`password`	password associated with your username

Value

the auth token associated with the username and password

Note

do not save your auth token in a public repository. For example, you might put it in your .Renviron and then make sure that your .Renviron is in your .gitignore. Otherwise, save it outside of a github tracked directory or otherwise ensure that it will not be pushed up to github

Examples

## Not run: 
# Get a user authentication token
token <- getUserAuthToken("https://example.com/auth", "myusername", "mypassword")
print(token)

# setting this into your environment
# read about using your .Renviron here
# https://support.posit.co/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf
# you can set this at either a user or project level. I suggest working
# in projects in general
usethis::edit_r_environ('project')

# this will open a file called .Renviron in your current project.

# IMPORTANT immediately create a .gitignore and add the like .Renviron
# to it, or you risk putting your login token onto github

# add your token to the .Renviron like this
# TOKEN=<your token>

# reload the project, and now you can access the environmental variable
# token
print(Sys.getenv('TOKEN'))

# Using the authentication token with httr
library(httr)
# if you have already put your token in your .Renviron, then you could
# access it like this:
token = Sys.getenv("TOKEN")
# otherwise, token is set as it is in the example above
my_api_call <- GET("https://example.com/api",
                   add_headers(Authorization = paste("token", token)))
content(my_api_call)

## End(Not run)

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.