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#' @title Read/Export records that populate a REDCap report
#'
#' @description Exports the data set of a report created on a project's
#' 'Data Exports, Reports, and Stats' page.
#'
#' @param redcap_uri The URI (uniform resource identifier) of the REDCap
#' project. Required.
#' @param token The user-specific string that serves as the password for a
#' project. Required.
#' @param report_id A single integer, provided next to the report name on the
#' report list page. Required.
#' @param raw_or_label A string (either `'raw'` or `'label'`) that specifies
#' whether to export the raw coded values or the labels for the options of
#' multiple choice fields. Default is `'raw'`.
#' @param raw_or_label_headers A string (either `'raw'` or `'label'` that
#' specifies for the CSV headers whether to export the variable/field names
#' (raw) or the field labels (label). Default is `'raw'`.
#' @param export_checkbox_label specifies the format of checkbox field values
#' specifically when exporting the data as labels. If `raw_or_label` is
#' `'label'` and `export_checkbox_label` is TRUE, the values will be the text
#' displayed to the users. Otherwise, the values will be 0/1.
# placeholder: returnFormat
#' @param col_types A [readr::cols()] object passed internally to
#' [readr::read_csv()]. Optional.
#' @param guess_type A boolean value indicating if all columns should be
#' returned as character. If false, [readr::read_csv()] guesses the intended
#' data type for each column. Ignored if `col_types` is not null.
#' @param guess_max A positive integer passed to [readr::read_csv()] that
#' specifies the maximum number of records to use for guessing column types.
#' @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 to pass to `POST` method in the
#' `httr` package. See the details below. Optional.
#'
#' @return Currently, a list is returned with the following elements:
#' * `data`: An R [base::data.frame()] of the desired records and columns.
#' * `success`: A boolean value indicating if the operation was apparently
#' successful.
#' * `status_code`: The
#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
#' of the operation.
#' * `outcome_message`: A human readable string indicating the operation's
#' outcome.
#' * `elapsed_seconds`: The duration of the function.
#' * `raw_text`: If an operation is NOT successful, the text returned by
#' REDCap. If an operation is successful, the `raw_text` is returned as an
#' empty string to save RAM.
#'
#' @details
#' The full list of configuration options accepted by the `httr` package is
#' viewable by executing [httr::httr_options()]. The `httr` package and
#' documentation is available at https://cran.r-project.org/package=httr.
#'
#' @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/"
#' token <- "9A81268476645C4E5F03428B8AC3AA7B"
#' report_1_id <- 5980L
#' report_2_id <- 6431L
#'
#' # Return all records and all variables.
#' ds_1a <-
#' REDCapR::redcap_report(
#' redcap_uri = uri,
#' token = token,
#' report_id = report_1_id
#' )$data
#'
#'
#' # Specify the column types.
#' col_types_1 <- readr::cols(
#' record_id = readr::col_integer(),
#' height = readr::col_double(),
#' health_complete = readr::col_integer(),
#' address = readr::col_character(),
#' ethnicity = readr::col_integer()
#' )
#' ds_1b <-
#' REDCapR::redcap_report(
#' redcap_uri = uri,
#' token = token,
#' report_id = report_1_id,
#' col_types = col_types_1
#' )$data
#'
#'
#' # Return condensed checkboxes Report option:
#' # "Combine checkbox options into single column of only the checked-off
#' # options (will be formatted as a text field when exported to
#' # stats packages)"
#' col_types_2 <- readr::cols(
#' record_id = readr::col_integer(),
#' race = readr::col_character()
#' )
#' ds_2 <-
#' REDCapR::redcap_report(
#' redcap_uri = uri,
#' token = token,
#' report_id = report_2_id,
#' col_types = col_types_2
#' )$data
#' }
#' @importFrom magrittr %>%
#' @export
redcap_report <- function(
redcap_uri,
token,
report_id,
raw_or_label = "raw",
raw_or_label_headers = "raw",
export_checkbox_label = FALSE,
col_types = NULL,
guess_type = TRUE,
guess_max = 1000L,
verbose = TRUE,
config_options = NULL
) {
checkmate::assert_character(redcap_uri , any.missing=FALSE, len=1, pattern="^.{1,}$")
checkmate::assert_character(token , any.missing=FALSE, len=1, pattern="^.{1,}$")
checkmate::assert_integerish(report_id , any.missing=FALSE, len=1, lower=1)
checkmate::assert_character(raw_or_label , any.missing=FALSE, len=1)
checkmate::assert_subset( raw_or_label , c("raw", "label"))
checkmate::assert_character(raw_or_label_headers , any.missing=FALSE, len=1)
checkmate::assert_subset( raw_or_label_headers , c("raw", "label"))
checkmate::assert_logical( export_checkbox_label , any.missing=FALSE, len=1)
checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
checkmate::assert_integerish(guess_max , any.missing=FALSE, len=1, lower=1)
checkmate::assert_logical( verbose , any.missing=FALSE, len=1, null.ok=TRUE)
checkmate::assert_list( config_options , any.missing=TRUE , null.ok=TRUE)
token <- sanitize_token(token)
verbose <- verbose_prepare(verbose)
post_body <- list(
token = token,
content = "report",
report_id = report_id,
format = "csv",
rawOrLabel = raw_or_label,
rawOrLabelHeaders = raw_or_label_headers,
exportCheckboxLabel = tolower(as.character(export_checkbox_label))
)
# This is the important line that communicates with the REDCap server.
kernel <- kernel_api(redcap_uri, post_body, config_options)
if (kernel$success) {
col_types <-
if (!is.null(col_types)) col_types
else if (guess_type) NULL
else readr::cols(.default = readr::col_character())
try(
# Convert the raw text to a dataset.
ds <-
readr::read_csv(
file = I(kernel$raw_text),
col_types = col_types,
guess_max = guess_max,
show_col_types = FALSE
) %>%
as.data.frame(),
# Don't print the warning in the try block. Print it below,
# where it's under the control of the caller.
silent = TRUE
)
if (exists("ds") & inherits(ds, "data.frame")) {
outcome_message <- sprintf(
"%s records and %s columns were read from REDCap in %0.1f seconds. The http status code was %i.",
format( nrow(ds), big.mark = ",", scientific = FALSE, trim = TRUE),
format(length(ds), big.mark = ",", scientific = FALSE, trim = TRUE),
kernel$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 { # ds doesn't exist as a data.frame.
# nocov start
# Override the 'success' determination from the http status code.
# and return an empty data.frame.
kernel$success <- FALSE
ds <- data.frame()
outcome_message <- sprintf(
"The REDCap report failed. The http status code was %i. The 'raw_text' returned was '%s'.",
kernel$status_code,
kernel$raw_text
)
# nocov end
}
} else { # kernel fails
ds <- data.frame() #Return an empty data.frame
outcome_message <- if (any(grepl(kernel$regex_empty, kernel$raw_text))) {
"The REDCapR report operation was not successful. The returned dataset was empty." # nocov
} else {
sprintf(
"The REDCapR report operation was not successful. The error message was:\n%s",
kernel$raw_text
)
}
}
if (verbose)
message(outcome_message)
list(
data = ds,
success = kernel$success,
status_code = kernel$status_code,
outcome_message = outcome_message,
report_id = report_id,
elapsed_seconds = kernel$elapsed_seconds,
raw_text = kernel$raw_text
)
}
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