nprcgenekeepr (version 2.0.0)

setLabKeyDefaults: Configure Rlabkey authentication for the current session

Description

Sets up the credentials that getDemographics (and any other Rlabkey call) uses to authenticate against the LabKey EHR server. An API key, when available, is preferred; otherwise the function falls back to a .netrc/_netrc file; when neither is present it stops with an actionable error rather than letting Rlabkey fail later with an opaque message.

Usage

setLabKeyDefaults(siteInfo = getSiteInfo())

Value

Invisibly, a list with elements method (one of "apiKey" or "netrc") and baseUrl. Stops with an error when no credential can be found.

Arguments

siteInfo

list of site information as returned by getSiteInfo. The elements used are baseUrl, configFile, homeDir, and sysname.

Details

The API key is sourced, in order of precedence, from

1. the environment variable NPRCGENEKEEPR_LABKEY_APIKEY, then

2. an apiKey entry in the nprcgenekeepr configuration file.

When an API key is found, labkey.setDefaults is called with that key and siteInfo$baseUrl. When no API key is found, the function checks for a netrc file (the NETRC environment variable, then the home-directory .netrc on non-Windows or _netrc on Windows) and, if present, leaves Rlabkey to use it. The API key is never read from or written to the package sources; keep it in the environment, the configuration file, or the netrc file only.

Examples

if (FALSE) {
## Requires an apiKey (env var or config) or a .netrc file to succeed.
library(nprcgenekeepr)
result <- tryCatch(
  setLabKeyDefaults(getSiteInfo(expectConfigFile = FALSE)),
  error = function(e) conditionMessage(e)
)
}