R/phenotypes.R

In ropensci/rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

#' Get openSNP phenotype data for one or multiple users.
#'
#' @export
#' @family opensnp-fxns
#' @param userid ID of openSNP user.
#' @param df Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
#' @param ... Curl options passed on to [crul::HttpClient]
#' @return List of phenotypes for specified user(s).
#'
#' @examples \dontrun{
#' phenotypes(userid = 1)
#' phenotypes(userid = "1,6,8", df = TRUE)
#' phenotypes(userid = "1-8", df = TRUE)
#'
#' # coerce to data.frame
#' library(plyr)
#' df <- ldply(phenotypes(userid = "1-8", df = TRUE))
#' head(df)
#' tail(df)
#'
#' # pass on curl options
#' phenotypes(1, verbose = TRUE)
#' }
phenotypes <- function(userid = NA, df = FALSE, ...) {
  url2 <- paste0(paste0(osnp_base(), "phenotypes/json/"), userid, ".json")
  
  tryCatch(
    {
      res <- os_GET(url2, list(), ...)
      ## need to check what it returns
      # Process the data or perform any desired operations
    },
    error = function(e) {
      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
    }
    ,
    warning = function(w) {
      message("Warning: Data retrieval resulted in a warning.")
      # Handle warnings if necessary
      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
    }
  )
  out <- jsonlite::fromJSON(res, FALSE)

  userid <- gsub("-", ",", userid)

  if (df) {
    if (length(str_split(userid, ",")[[1]]) == 1) {
      tmp <- ldply(out[[2]], data.frame, stringsAsFactors = FALSE)
      names(tmp) <- c("phenotype", "phenotypeID", "variation")
      tmp
    } else {
      outdf <- list()
      for (i in seq_along(out)) {
        if (inherits(try(out[[i]][[2]], silent = TRUE), "try-error")) {
          df <- data.frame("no data", "no data", "no data",
            stringsAsFactors = FALSE
          )
          names(df) <- c("phenotype", "phenotypeID", "variation")
          outdf[[paste("no info on user", i, sep = "_")]] <- df
        } else {
          if (length(out[[i]][[2]]) == 0) {
            df <- data.frame("no data", "no data", "no data",
              stringsAsFactors = FALSE
            )
            names(df) <- c("phenotype", "phenotypeID", "variation")
            outdf[[out[[i]][[1]][["name"]]]] <- df
          } else {
            df <- ldply(out[[i]][[2]], data.frame, stringsAsFactors = FALSE)
            names(df) <- c("phenotype", "phenotypeID", "variation")
            outdf[[out[[i]][[1]][["name"]]]] <- df
          }
        }
      }
      outdf
    }
  } else {
    out
  }
}