R/tgrAnnotate.R

In FredHutch/tgR: TGR Convenience Functions

#' Queries TGR REDCap for dataset annotations
#'
#' @param harmonizedOnly (Optional) Whether you want only the annotations that are harmonized across all projects (TRUE) or a complete data set (FALSE, default).
#' @param evenEmptyCols (Optional) Whether you want even the empty fields in your final data frame (TRUE) or if you just want columns where there is at least one value in the resulting dataset (FALSE, default).
#' @param DAG (admin only) A character vector contining the name(s) of the TGR data access group(s) for which to request data, or "all".
#' @return Returns a long form data frame containing the requested dataset.
#' @author Amy Paguirigan
#' @details
#' Requires setCreds() to have been run successfully.
#' @export
tgrAnnotate <- function(DAG = NULL, harmonizedOnly = FALSE, evenEmptyCols = FALSE) {
  if ("" %in% Sys.getenv(c("REDURI", "TGR"))) {
    stop("You have missing environment variables.  Please setCreds().")}
  else message("Credentials set successfully.")
        tgrData <- suppressMessages(
          a<- REDCapR::redcap_read_oneshot(
          Sys.getenv("REDURI"), Sys.getenv("TGR"),
          export_data_access_groups = T, guess_type = F)$data %>%
          dplyr::select(-dplyr::ends_with("_complete")))

        if (harmonizedOnly == TRUE) {
          harmfields <- suppressMessages(
            REDCapR::redcap_metadata_read(Sys.getenv("REDURI"), Sys.getenv("TGR"))$data)
          Keep <- harmfields %>% dplyr::filter(grepl("tgr_*", form_name)==T) %>% dplyr::select(field_name)
          tgrData <- tgrData %>% dplyr::select(dplyr::one_of("molecular_id", "redcap_data_access_group", Keep$field_name))
        }
        tgrData[tgrData == ""] <- NA
    if (is.null(DAG) == T ) {message("Returning all data you have access to.")
    } else {
        if (DAG == "all") {message("Returning all data you have access to.")
          message(paste0("DAGs returned: ", paste(unique(tgrData$redcap_data_access_group), collapse = ", ")))
        } else {
          if (DAG %in% tgrData$redcap_data_access_group){
            tgrData <- tgrData %>% dplyr::filter(redcap_data_access_group %in% DAG)
            message(paste0("DAGs returned: ", paste(unique(tgrData$redcap_data_access_group), collapse = ", ")))
          } else {stop("Invalid DAG or you do not have permissions to that DAG.")}
        }
    }
    if (evenEmptyCols == F) {
      tgrData <- tgrData %>%
        Filter(function(x)!all(is.na(x)), .) %>%
        Filter(function(x)!all(x==0), .)
    }
    return(tgrData)
}