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#' @title
#' Export the metadata of a REDCap project
#'
#' @description
#' Export the metadata (as a data dictionary) of a REDCap project
#' as a [tibble::tibble()]. Each row in the data dictionary corresponds to
#' one field in the project's dataset.
#'
#' @param redcap_uri The
#' [uri](https://en.wikipedia.org/wiki/Uniform_Resource_Identifier)/url
#' of the REDCap server
#' typically formatted as "https://server.org/apps/redcap/api/".
#' Required.
#' @param token The user-specific string that serves as the password for a
#' project. Required.
#' @param forms An array, where each element corresponds to the REDCap form
#' of the desired fields. Optional.
#' @param fields An array, where each element corresponds to a desired project
#' field. Optional.
#' @param verbose A boolean value indicating if `message`s should be printed
#' to the R console during the operation. The verbose output might contain
#' sensitive information (*e.g.* PHI), so turn this off if the output might
#' be visible somewhere public. Optional.
#' @param config_options A list of options passed to [httr::POST()].
#' See details at [httr::httr_options()]. Optional.
#' @param handle_httr The value passed to the `handle` parameter of
#' [httr::POST()].
#' This is useful for only unconventional authentication approaches. It
#' should be `NULL` for most institutions. Optional.
#'
#' @return
#' Currently, a list is returned with the following elements:
#'
#' * `data`: An R [tibble::tibble()] of the desired fields (as rows).
#' * `success`: A boolean value indicating if the operation was apparently
#' successful.
#' * `status_codes`: A collection of
#' [http status codes](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes),
#' separated by semicolons. There is one code for each batch attempted.
#' * `outcome_messages`: A collection of human readable strings indicating the
#' operations' semicolons. There is one code for each batch attempted. In an
#' unsuccessful operation, it should contain diagnostic information.
#' * `forms_collapsed`: The desired records IDs, collapsed into a single
#' string, separated by commas.
#' * `fields_collapsed`: The desired field names, collapsed into a single
#' string, separated by commas.
#' * `elapsed_seconds`: The duration of the function.
#'
#' @author
#' Will Beasley
#'
#' @references
#' The official documentation can be found on the 'API Help Page'
#' and 'API Examples' pages on the REDCap wiki (*i.e.*,
#' https://community.projectredcap.org/articles/456/api-documentation.html and
#' https://community.projectredcap.org/articles/462/api-examples.html).
#' If you do not have an account for the wiki, please ask your campus REDCap
#' administrator to send you the static material.
#'
#' @examples
#' \dontrun{
#' uri <- "https://bbmc.ouhsc.edu/redcap/api/"
#'
#' # A simple project (pid 153)
#' token <- "9A81268476645C4E5F03428B8AC3AA7B"
#' REDCapR::redcap_metadata_read(redcap_uri=uri, token=token)
#'
#' # A longitudinal project (pid 212)
#' token <- "0434F0E9CF53ED0587847AB6E51DE762"
#' REDCapR::redcap_metadata_read(redcap_uri=uri, token=token)
#'
#' # A repeating measures (pid 3181)
#' token <- "22C3FF1C8B08899FB6F86D91D874A159"
#' REDCapR::redcap_metadata_read(redcap_uri=uri, token=token)
#' }
#' @importFrom magrittr %>%
#' @export
redcap_metadata_read <- function(
redcap_uri,
token,
forms = NULL,
fields = NULL,
verbose = TRUE,
config_options = NULL,
handle_httr = NULL
) {
checkmate::assert_character(redcap_uri , any.missing=FALSE, len=1, pattern="^.{1,}$")
checkmate::assert_character(token , any.missing=FALSE, len=1, pattern="^.{1,}$")
assert_field_names(fields)
token <- sanitize_token(token)
fields_collapsed <- collapse_vector(fields)
fields_array <- to_api_array(fields, "fields")
forms_collapsed <- collapse_vector(forms)
forms_array <- to_api_array(forms, "forms")
verbose <- verbose_prepare(verbose)
post_body <- list(
token = token,
content = "metadata",
format = "json"
)
# append forms and fields arrays in format expected by REDCap API
# If either is NULL nothing will be appended
post_body <- c(post_body, fields_array, forms_array)
# This is the important call that communicates with the REDCap server.
kernel <-
kernel_api(
redcap_uri = redcap_uri,
post_body = post_body,
config_options = config_options,
handle_httr = handle_httr
)
if (kernel$success) {
try(
{
# Convert the raw text to a dataset.
ds <-
kernel$raw_text %>%
jsonlite::fromJSON(
flatten = TRUE
) %>%
tibble::as_tibble() %>%
dplyr::mutate_all(
~dplyr::na_if(.x, "")
)
},
# Don't print the warning in the try block. Print it below,
# where it's under the control of the caller.
silent = TRUE
)
if (exists("ds") && inherits(ds, "data.frame")) {
outcome_message <- sprintf(
"The data dictionary describing %s fields was read from REDCap in %0.1f seconds. The http status code was %i.",
format(nrow(ds), big.mark = ",", scientific = FALSE, trim = TRUE),
kernel$elapsed_seconds,
kernel$status_code
)
# If an operation is successful, the `raw_text` is no longer returned
# to save RAM. The content is not really necessary with httr's status
# message exposed.
kernel$raw_text <- ""
} else { # nocov start
# Override the 'success' determination from the http status code
# and return an empty data.frame.
kernel$success <- FALSE
ds <- tibble::tibble()
outcome_message <- sprintf(
"The REDCap metadata export failed. The http status code was %i. The 'raw_text' returned was '%s'.",
kernel$status_code,
kernel$raw_text
)
} # nocov end
} else {
# nocov start
ds <- tibble::tibble() # Return an empty data.frame
outcome_message <- sprintf(
"The REDCapR metadata export operation was not successful. The error message was:\n%s",
kernel$raw_text
)
# nocov end
}
if (verbose)
message(outcome_message)
list(
data = ds,
success = kernel$success,
status_code = kernel$status_code,
outcome_message = outcome_message,
forms_collapsed = forms_collapsed,
fields_collapsed = fields_collapsed,
elapsed_seconds = kernel$elapsed_seconds,
raw_text = kernel$raw_text
)
}
#' @title
#' Convert a vector to the array format expected by the REDCap API
#'
#' @description
#' Utility function to convert a vector into the array format expected by the
#' some REDCap API calls. It is called internally by REDCapR functions,
#' and is not intended to be called directly.
#'
#' @param x A vector to convert to array format. Can be `NULL`.
#' @param element_names A string containing the name of the API request parameter for
#' the array. Must be either "fields" or "forms".
#'
#' @return
#' If `x` is not `NULL` a list is returned with one element for
#' each element of x in the format:
#' \code{list(`element_names[0]` = x[1], `element_names[1]` = x[2], ...)}.
#'
#' If `x` is `NULL` then `NULL` is returned.
to_api_array <- function(x, element_names) {
checkmate::assert_character(x , null.ok = TRUE, any.missing = FALSE)
checkmate::assert_character(element_names, null.ok = TRUE, any.missing = FALSE, max.len = 1L, pattern = "^fields|forms$")
if (is.null(x)) {
return(NULL)
} else if (is.null(element_names)) {
rlang::abort("The `element_names` parameter cannot be null if `x` is not null.")
}
res <- as.list(x)
names(res) <- paste0(element_names, "[", seq_along(res) - 1L, "]")
res
}
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