Download concept sets from ATLAS and save them in the package.

Retrieves each concept set definition from the ATLAS WebAPI, cleans the concept set name for use as a file name and writes the JSON definition to inst/concept_sets/<conceptSetType>/.

Usage

pullConceptsAtlas(
  conceptSetList,
  conceptSetType,
  baseUrl = "https://atlas.darwin-eu.org/WebAPI",
  deletePrevious = TRUE,
  patternToRemove = c("p[0-9]{1}_c[0-9]{1}_[0-9]{3}_"),
  authHeader = Sys.getenv("ATLAS_TOKEN")
)

Arguments

conceptSetList

A numeric vector of ATLAS concept set IDs to download.

conceptSetType

A character string used to group the downloaded concept set JSON files under inst/concept_sets/.

baseUrl

A character string with the base URL of the ATLAS WebAPI.

deletePrevious

A logical value indicating whether to delete existing files in the target <conceptSetType> folder before downloading the new concept sets.

patternToRemove

A vector of regular expressions containing the pattern(s) to be removed from the ATLAS concept set names before creating the output JSON files.

authHeader

Authorization header for the WebAPI. Defaults to Sys.getenv("ATLAS_TOKEN"). Use "" for a public WebAPI.

Value

A tibble with one row per downloaded concept set and the columns conceptSetId, originalName, cleanName, and fileName.

Details

Requires the optional CRAN packages httr, RJSONIO, lubridate, and rlang. For a protected WebAPI, set ATLAS_TOKEN in your local .Renviron file and restart R. The token may include the Bearer prefix. It is sent only to the supplied WebAPI. Do not commit the token to version control. The internal retrieval helpers are adapted from OHDSI's ROhdsiWebApi under the Apache License 2.0; see inst/COPYRIGHTS in the package source.

Examples

if (FALSE) { # \dontrun{
# Requires a connection to the ATLAS WebAPI
conceptSetList <- c(12345)
conceptSetType <- "example"
pullConceptsAtlas(
   conceptSetList = conceptSetList,
   conceptSetType = conceptSetType,
   baseUrl = "https://atlas.darwin-eu.org/WebAPI",
   deletePrevious = TRUE,
   patternToRemove = c("p[0-9]{1}_c[0-9]{1}_[0-9]{3}_") 
)
} # }