#' Retrieve project API key if stored, if not, set and retrieve #' #' @param key.name character vector of key name #' #' @return character vector #' @importFrom keyring key_list key_get key_set #' @export get_api_key <- function(key.name) { if (key.name %in% keyring::key_list()$service) { keyring::key_get(service = key.name) } else { keyring::key_set(service = key.name, prompt = "Provide REDCap API key:") keyring::key_get(service = key.name) } } #' Secure API key storage and data acquisition in one #' #' @param project.name The name of the current project (for key storage with #' `keyring::key_set()`, using the default keyring) #' @param widen.data argument to widen the exported data #' @param uri REDCap database API uri #' @param ... arguments passed on to `REDCapCAST::read_redcap_tables()` #' #' @return data.frame or list depending on widen.data #' @export easy_redcap <- function(project.name, widen.data = TRUE, uri, ...) { key <- get_api_key(key.name = paste0(project.name, "_REDCAP_API")) out <- read_redcap_tables( uri = uri, token = key, ... ) if (widen.data) { out <- out |> redcap_wider() } out } #' REDCap read function to preserve field labels and all factor levels #' #' @description #' This works very much as `read_redcap_tables()` and might end up there #' #' #' @param uri REDCap database API uri #' @param token API token #' @param records records to download #' @param fields fields to download #' @param events events to download #' @param forms forms to download #' @param split_forms Whether to split "repeating" or "all" forms, default is #' "all". #' #' @return data.frame or list #' @export #' read_redcap_labelled <- function(uri, token, records = NULL, fields = NULL, events = NULL, forms = NULL, split_forms = "all") { m <- REDCapR::redcap_metadata_read(redcap_uri = uri, token = token)[["data"]] # Tests if (!is.null(fields)) { fields_test <- fields %in% c(m$field_name, paste0(unique(m$form_name), "_complete")) if (any(!fields_test)) { print(paste0( "The following field names are invalid: ", paste(fields[!fields_test], collapse = ", "), "." )) stop("Not all supplied field names are valid") } } if (!is.null(forms)) { forms_test <- forms %in% unique(m$form_name) if (any(!forms_test)) { print(paste0( "The following form names are invalid: ", paste(forms[!forms_test], collapse = ", "), "." )) stop("Not all supplied form names are valid") } } if (!is.null(events)) { arm_event_inst <- REDCapR::redcap_event_instruments( redcap_uri = uri, token = token ) event_test <- events %in% unique(arm_event_inst$data$unique_event_name) if (any(!event_test)) { print(paste0( "The following event names are invalid: ", paste(events[!event_test], collapse = ", "), "." )) stop("Not all supplied event names are valid") } } # Getting dataset d <- REDCapR::redcap_read( redcap_uri = uri, token = token, fields = fields, events = events, forms = forms, records = records, raw_or_label = "raw" )[["data"]] # Applying labels d <- purrr::imap(d, \(.x, .i){ if (.i %in% m$field_name) { # Does not handle checkboxes out <- set_attr(.x, label = clean_field_label(m$field_label[m$field_name == .i]), attr = "label" ) out } else { .x } }) |> dplyr::bind_cols() d <- purrr::imap(d, \(.x, .i){ if (any(c("radio", "dropdown") %in% m$field_type[m$field_name == .i])) { format_redcap_factor(.x, m$select_choices_or_calculations[m$field_name == .i]) } else { .x } }) |> dplyr::bind_cols() # Process repeat instrument naming # Removes any extra characters other than a-z, 0-9 and "_", to mimic raw # instrument names. if ("redcap_repeat_instrument" %in% names(d)) { d$redcap_repeat_instrument <- clean_redcap_name(d$redcap_repeat_instrument) } # Processing metadata to reflect focused dataset m <- focused_metadata(m, names(d)) # Splitting out <- REDCap_split(d, m, forms = split_forms, primary_table_name = "" ) sanitize_split(out) } #' Very simple function to remove rich text formatting from field label #' and save the first paragraph ('
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'). #' #' @param data field label #' #' @return character vector #' @export #' #' @examples #' clean_field_label("Fazekas score