REDCapR: Interaction Between R and REDCap

Documented in redcap_read_oneshot_eav

#' @title
#' Read/Export records from a REDCap project --still in development
#'
#' @description
#' This function uses REDCap's API to select and return data.
#' This function is still in development.
#'
#' @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 records An array, where each element corresponds to the ID of a
#' desired record.  Optional.
#' @param fields An array, where each element corresponds to a desired
#' project field.  Optional.
#' @param forms An array, where each element corresponds to a desired project
#' field.  Optional.
#' @param events An array, where each element corresponds to a desired project
#' event.  Optional.
#' @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'`.
# placeholder: exportCheckboxLabel
# placeholder: returnFormat
# placeholder: export_survey_fields
#' @param export_data_access_groups A boolean value that specifies whether or
#' not to export the `redcap_data_access_group` field when data access groups
#' are utilized in the project. Default is `FALSE`. See the details below.
#' @param filter_logic String of logic text (e.g., `[gender] = 'male'`) for
#' filtering the data to be returned by this API method, in which the API
#' will only return the records (or record-events, if a longitudinal project)
#' where the logic evaluates as TRUE.   An blank/empty string returns all
#' records.
#' @param datetime_range_begin To return only records that have been created or
#' modified *after* a given datetime, provide a
#' [POSIXct]
#' (https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html)
#' value.
#' If not specified, REDCap will assume no begin time.
#' @param datetime_range_end To return only records that have been created or
#' modified *before* a given datetime, provide a
#' [POSIXct]
#' (https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html)
#' value.
#' If not specified, REDCap will assume no end time.
#' @param blank_for_gray_form_status A boolean value that specifies whether
#' or not to export blank values for instrument complete status fields that have
#' a gray status icon. All instrument complete status fields having a gray icon
#' can be exported either as a blank value or as "0" (Incomplete). Blank values
#' are recommended in a data export if the data will be re-imported into a
#' REDCap project. Default is `FALSE`.
#'
#' @param http_response_encoding  The encoding value passed to
#' [httr::content()].  Defaults to 'UTF-8'.
#' @param locale a [readr::locale()] object to specify preferences like
#' number, date, and time formats.  This object is passed to
#' [readr::read_csv()].  Defaults to [readr::default_locale()].
#' @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`: A [tibble::tibble()] 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.
#' * `records_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.
#' * `filter_logic`: The filter statement passed as an argument.
#' * `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
#' If you do not pass in this export_data_access_groups value, it will
#' default to `FALSE`. The following is from the API help page for version
#' 5.2.3:
#' This flag is only viable if the user whose token is being used to make
#' the API request is *not* in a data access group. If the user is in a
#' group, then this flag will revert to its default value.
#'
#' As of REDCap 6.14.3, this field is not exported in the EAV API call.
#'
#' @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"
#'
#' # Return all records and all variables.
#' ds <- REDCapR:::redcap_read_oneshot_eav(redcap_uri=uri, token=token)$data
#'
#' # Return only records with IDs of 1 and 3
#' desired_records_v1 <- c(1, 3)
#' ds_some_rows_v1    <- REDCapR:::redcap_read_oneshot_eav(
#'    redcap_uri = uri,
#'    token      = token,
#'    records    = desired_records_v1
#' )$data
#'
#' # Return only the fields record_id, name_first, and age
#' desired_fields_v1 <- c("record_id", "name_first", "age")
#' ds_some_fields_v1 <- REDCapR:::redcap_read_oneshot_eav(
#'    redcap_uri = uri,
#'    token      = token,
#'    fields     = desired_fields_v1
#' )$data
#'}

#' @importFrom magrittr %>%
#' @importFrom utils type.convert
#' @importFrom rlang .data
# @export  # Not currently exported.
redcap_read_oneshot_eav <- function(
  redcap_uri,
  token,
  records                       = NULL,
  fields                        = NULL,
  forms                         = NULL,
  events                        = NULL,
  raw_or_label                  = "raw",
  raw_or_label_headers          = "raw",
  # placeholder: exportCheckboxLabel
  # placeholder: returnFormat
  # placeholder: export_survey_fields
  export_data_access_groups     = FALSE,
  filter_logic                  = "",
  datetime_range_begin          = as.POSIXct(NA),
  datetime_range_end            = as.POSIXct(NA),
  blank_for_gray_form_status    = FALSE,

  # placeholder: guess_type
  # placeholder: guess_max
  http_response_encoding        = "UTF-8",
  locale                        = readr::default_locale(),
  verbose                       = TRUE,
  config_options                = NULL,
  handle_httr                   = NULL
) {

  checkmate::assert_character(redcap_uri                , any.missing=FALSE, len=1, pattern="^.{1,}$")
  checkmate::assert_character(token                     , any.missing=FALSE, len=1, pattern="^.{1,}$")
  checkmate::assert_atomic(records                      , any.missing=TRUE , min.len=0)
  checkmate::assert_character(fields                    , any.missing=TRUE , min.len=1, pattern="^.{1,}$", null.ok=TRUE )
  checkmate::assert_character(forms                     , any.missing=TRUE , min.len=1, pattern="^.{1,}$", null.ok=TRUE )
  checkmate::assert_character(events                    , any.missing=TRUE , min.len=1, pattern="^.{1,}$", null.ok=TRUE )
  checkmate::assert_character(raw_or_label              , any.missing=FALSE, len=1)
  checkmate::assert_subset(   raw_or_label              , c("raw", "label"))
  checkmate::assert_character(raw_or_label_headers      , any.missing=FALSE, len=1)
  checkmate::assert_subset(   raw_or_label_headers      , c("raw", "label"))
  # placeholder: export_checkbox_label --irrelevant in EAV
  # placeholder: returnFormat
  # placeholder: export_survey_fields
  checkmate::assert_logical(  export_data_access_groups , any.missing=FALSE, len=1)
  checkmate::assert_character(filter_logic              , any.missing=FALSE, len=1, pattern="^.{0,}$")
  checkmate::assert_posixct(  datetime_range_begin      , any.missing=TRUE , len=1, null.ok=TRUE)
  checkmate::assert_posixct(  datetime_range_end        , any.missing=TRUE , len=1, null.ok=TRUE)
  checkmate::assert_logical( blank_for_gray_form_status , any.missing=FALSE, len=1)

  # placeholder: checkmate::assert_logical(  guess_type                , any.missing=FALSE, len=1)
  # placeholder: checkmate::assert_numeric(  guess_max                , any.missing=FALSE, len=1, lower=1)
  checkmate::assert_character(http_response_encoding    , any.missing=FALSE,     len=1)
  checkmate::assert_class(    locale, "locale"          , null.ok = FALSE)
  checkmate::assert_logical(  verbose                   , any.missing=FALSE, len=1, null.ok=TRUE)
  checkmate::assert_list(     config_options            , any.missing=TRUE ,        null.ok=TRUE)

  assert_field_names(fields)

  token                     <- sanitize_token(token)
  records_collapsed         <- collapse_vector(records)
  fields_collapsed          <- collapse_vector(fields)
  forms_collapsed           <- collapse_vector(forms)
  events_collapsed          <- collapse_vector(events)
  export_data_access_groups <- ifelse(export_data_access_groups, "true", "false")
  filter_logic              <- filter_logic_prepare(filter_logic)
  datetime_range_begin      <- dplyr::coalesce(strftime(datetime_range_begin, "%Y-%m-%d %H:%M:%S"), "")
  datetime_range_end        <- dplyr::coalesce(strftime(datetime_range_end  , "%Y-%m-%d %H:%M:%S"), "")
  verbose                   <- verbose_prepare(verbose)

  post_body <- list(
    token                        = token,
    content                      = "record",
    format                       = "csv",
    type                         = "eav",
    rawOrLabel                   = raw_or_label,
    rawOrLabelHeaders            = raw_or_label_headers,
    exportDataAccessGroups       = export_data_access_groups,
    filterLogic                  = filter_logic,
    dateRangeBegin               = datetime_range_begin,
    dateRangeEnd                 = datetime_range_end,
    exportBlankForGrayFormStatus = blank_for_gray_form_status
    # record, fields, forms & events are specified below
  )

  if (0L < nchar(records_collapsed)) post_body$records  <- records_collapsed
  if (0L < nchar(fields_collapsed )) post_body$fields   <- fields_collapsed
  if (0L < nchar(forms_collapsed  )) post_body$forms    <- forms_collapsed
  if (0L < nchar(events_collapsed )) post_body$events   <- events_collapsed

  # 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,
    encoding        = http_response_encoding,
    handle_httr     = handle_httr
  )

  if (!kernel$success) {
    error_message     <- sprintf(
      "The REDCapR record export operation was not successful.  The error message was:\n%s",
      kernel$raw_text
    )
    stop(error_message)
  }

  ds_metadata <-
    REDCapR::redcap_metadata_read(
      redcap_uri,
      token,
      forms           = forms,
      handle_httr     = handle_httr,
      verbose         = verbose
    )$data

  ds_variable <-
    REDCapR::redcap_variables(
      redcap_uri  = redcap_uri,
      token       = token,
      handle_httr = handle_httr,
      verbose     = verbose
    )$data

  if (kernel$success) {
    try(
      {
        ds_eav <-
          readr::read_csv(
            file            = I(kernel$raw_text),
            locale          = locale,
            show_col_types  = FALSE
          )

        if (!"event_id" %in% colnames(ds_eav)) {
          ds_eav$event_id <- "dummy_1"
        }

        ds_metadata_expanded <-
          ds_metadata %>%
          dplyr::select("field_name", "select_choices_or_calculations", "field_type") %>%
          dplyr::mutate(
            is_checkbox   = (.data$field_type == "checkbox"),
            ids           = dplyr::if_else(.data$is_checkbox, .data$select_choices_or_calculations, "1"),
            ids           = gsub("(\\w+),.+?(\\||$)", "\\1", .data$ids),
            ids           = strsplit(.data$ids, " ")
          ) %>%
          dplyr::select(-"select_choices_or_calculations", -"field_type") %>%
          tidyr::unnest("ids") %>%
          dplyr::transmute(
            .data$is_checkbox,
            field_name          = dplyr::if_else(.data$is_checkbox, paste0(.data$field_name, "___", .data$ids), .data$field_name)
          ) %>%
          tibble::as_tibble()

        distinct_checkboxes <-
          ds_metadata_expanded %>%
          dplyr::filter(.data$is_checkbox) %>%
          dplyr::pull(.data$field_name)

        ds_possible_checkbox_rows  <-
          tidyr::crossing(
            field_name = distinct_checkboxes,
            record     = unique(ds_eav$record),
            field_type = "checkbox",
            event_id   =  unique(ds_eav$event_id)
          )

        variables_to_keep <-
          ds_metadata_expanded %>%
          dplyr::select("field_name") %>%
          dplyr::union(
            ds_variable %>%
              dplyr::select(field_name = "export_field_name") %>%
              dplyr::filter(grepl("^\\w+?_complete$", .data$field_name))
          ) %>%
          dplyr::pull(.data$field_name) #%>% rev()

        ds_eav_2 <-
          ds_eav %>%
          dplyr::left_join(
            ds_metadata %>%
              dplyr::select("field_name", "field_type"),
            by = "field_name"
          ) %>%
          dplyr::mutate(
            field_name = dplyr::if_else(!is.na(.data$field_type) & (.data$field_type == "checkbox"), paste0(.data$field_name, "___", .data$value), .data$field_name)
          ) %>%
          dplyr::full_join(ds_possible_checkbox_rows, by=c("record", "field_name", "field_type", "event_id")) %>%
          dplyr::mutate(
            value      = dplyr::if_else(!is.na(.data$field_type) & (.data$field_type == "checkbox"), as.character(!is.na(.data$value)), .data$value)
          )

        . <- NULL # For the sake of avoiding an R CMD check note.
        ds <-
          ds_eav_2 %>%
          dplyr::select(-"field_type") %>%
          # dplyr::select(-"redcap_repeat_instance") %>%        # TODO: need a good fix for repeats
          # tidyr::drop_na(event_id) %>%                            # TODO: need a good fix for repeats
          tidyr::spread(key = .data$field_name, value = .data$value) %>%
          dplyr::select(.data = ., !!intersect(variables_to_keep, colnames(.)))

        ds_2 <-
          ds %>%
          dplyr::mutate_if(is.character, ~type.convert(., as.is = FALSE)) %>%
          dplyr::mutate_if(is.factor   , as.character)
      },
      silent = TRUE # Don't print the warning in the try block.  Print it below, where it's under the control of the caller.
    )

    if (ifelse(exists("ds_2"), inherits(ds_2, "data.frame"), FALSE)) {
      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
      )

      kernel$raw_text   <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
    } else {
      # nocov start
      kernel$success    <- FALSE # Override the 'success' determination from the http status code.
      ds_2              <- tibble::tibble() # Return an empty data.frame
      outcome_message   <- sprintf(
        "The REDCap read failed.  The http status code was %s.  The 'raw_text' returned was '%s'.",
        kernel$status_code,
        kernel$raw_text
      )
      # nocov end
    }
  } else {
    # nocov start
    ds_2            <- tibble::tibble() # Return an empty data.frame
    outcome_message <-
      if (any(grepl(kernel$regex_empty, kernel$raw_text))) {
        "The REDCapR read/export operation was not successful.  The returned dataset was empty."
      } else {
        sprintf(
          "The REDCapR read/export operation was not successful.  The error message was:\n%s",
          kernel$raw_text
        )
      }
    # nocov end
  }

  if (verbose)
    message(outcome_message)

  list(
    data                  = ds_2,
    success               = kernel$success,
    status_code           = kernel$status_code,
    outcome_message       = outcome_message,
    records_collapsed     = records_collapsed,
    fields_collapsed      = fields_collapsed,
    filter_logic          = filter_logic,
    datetime_range_begin  = datetime_range_begin,
    datetime_range_end    = datetime_range_end,
    events_collapsed      = events_collapsed,
    elapsed_seconds       = kernel$elapsed_seconds,
    raw_text              = kernel$raw_text
  )
}