R/redcap-read-oneshot-eav.R

Defines functions redcap_read_oneshot_eav

Documented in redcap_read_oneshot_eav

#' @name redcap_read_oneshot_eav
# @export 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 (uniform resource identifier) of the REDCap project.  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 records_collapsed A single string, where the desired ID values are separated by commas.  Optional.
#' @param fields An array, where each element corresponds to a desired project field.  Optional.
#' @param fields_collapsed A single string, where the desired field names are separated by commas.  Optional.
#' @param forms An array, where each element corresponds to a desired project field.  Optional.
#' @param forms_collapsed A single string, where the desired form names are separated by commas.  Optional.
#' @param events An array, where each element corresponds to a desired project event.  Optional.
#' @param events_collapsed A single string, where the desired event names are separated by commas.  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 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](http://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.
#'
#' @importFrom magrittr %>%
#' @importFrom utils type.convert
#' @importFrom rlang .data
#'
#' @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.
#'
#' 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 (ie, 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 <- redcap_read_oneshot_eav(
#'    redcap_uri = uri,
#'    token      = token,
#'    fields     = desired_fields_v1
#' )$data
#'}

redcap_read_oneshot_eav <- function(
  redcap_uri,
  token,
  records                       = NULL, records_collapsed = "",
  fields                        = NULL, fields_collapsed  = "",
  forms                         = NULL, forms_collapsed   = "",
  events                        = NULL, events_collapsed  = "",
  raw_or_label                  = "raw",
  raw_or_label_headers          = "raw",
  # placeholder: exportCheckboxLabel
  # placeholder: returnFormat
  # placeholder: export_survey_fields
  export_data_access_groups     = FALSE,
  filter_logic                  = "",

  # placeholder: guess_type
  # placeholder: guess_max
  verbose                       = TRUE,
  config_options                = NULL
) {

  checkmate::assert_character(redcap_uri                , any.missing=F, len=1, pattern="^.{1,}$")
  checkmate::assert_character(token                     , any.missing=F, len=1, pattern="^.{1,}$")
  checkmate::assert_atomic(records                      , any.missing=T, min.len=0)
  checkmate::assert_character(records_collapsed         , any.missing=T, len=1, pattern="^.{0,}$", null.ok=T)
  checkmate::assert_character(fields                    , any.missing=T, min.len=1, pattern="^.{1,}$", null.ok=T)
  checkmate::assert_character(fields_collapsed          , any.missing=T, len=1, pattern="^.{0,}$", null.ok=T)
  checkmate::assert_character(forms                     , any.missing=T, min.len=1, pattern="^.{1,}$", null.ok=T)
  checkmate::assert_character(forms_collapsed           , any.missing=T, len=1, pattern="^.{0,}$", null.ok=T)
  checkmate::assert_character(events                    , any.missing=T, min.len=1, pattern="^.{1,}$", null.ok=T)
  checkmate::assert_character(events_collapsed          , any.missing=T, len=1, pattern="^.{0,}$", null.ok=T)
  checkmate::assert_character(raw_or_label              , any.missing=F, len=1)
  checkmate::assert_subset(   raw_or_label              , c("raw", "label"))
  checkmate::assert_character(raw_or_label_headers      , any.missing=F, len=1)
  checkmate::assert_subset(   raw_or_label_headers      , c("raw", "label"))
  # placeholder: export_checkbox_label --irrelevant in EAV
  # placeholder: returnFormat
  # placeholder: export_survey_fields
  checkmate::assert_logical(  export_data_access_groups , any.missing=F, len=1)
  checkmate::assert_character(filter_logic              , any.missing=F, len=1, pattern="^.{0,}$")
  #
  # placeholder: checkmate::assert_logical(  guess_type                , any.missing=F, len=1)
  # placeholder: checkmate::assert_integerish(guess_max                , any.missing=F, len=1, lower=1)
  checkmate::assert_logical(  verbose                   , any.missing=F, len=1, null.ok=T)
  checkmate::assert_list(     config_options            , any.missing=T, len=1, null.ok=T)

  validate_field_names(fields)

  token               <- sanitize_token(token)
  records_collapsed   <- collapse_vector(records  , records_collapsed)
  fields_collapsed    <- collapse_vector(fields   , fields_collapsed)
  forms_collapsed     <- collapse_vector(forms    , forms_collapsed)
  events_collapsed    <- collapse_vector(events   , events_collapsed)
  export_data_access_groups <- ifelse(export_data_access_groups, "true", "false")
  filter_logic        <- filter_logic_prepare(filter_logic)
  verbose             <- verbose_prepare(verbose)

  if( any(grepl("[A-Z]", fields_collapsed)) )
    warning("The fields passed to REDCap appear to have at least uppercase letter.  REDCap variable names are snake case.")

  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
    # record, fields, forms & events are specified below
  )

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

  # This is the important line that communicates with the REDCap server.
  kernel      <- kernel_api(redcap_uri, post_body, config_options)

  ds_metadata <- REDCapR::redcap_metadata_read(redcap_uri, token, forms_collapsed=forms_collapsed)$data
  ds_variable <- REDCapR::redcap_variables(redcap_uri, token)$data

  if( kernel$success ) {
    try (
      {
        ds_eav <- readr::read_csv(kernel$raw_text)

        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$select_choices_or_calculations, "1"),
            ids           = gsub("(\\d+),.+?(\\||$)", "\\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_("is_checkbox") %>%
          dplyr::pull(.data$field_name)

        ds_possible_checkbox_rows  <-
          tidyr::crossing(
            field_name = distinct_checkboxes,
            record     = dplyr::distinct(ds_eav, .data$record),
            field_type = "checkbox",
            event_id   = dplyr::distinct(ds_eav, .data$event_id)
          )

        variables_to_keep <- ds_metadata_expanded %>%
          dplyr::select(.data$field_name) %>%
          dplyr::union(
            ds_variable %>%
              dplyr::select_("field_name" = "export_field_name") %>%
              dplyr::filter(grepl("^\\w+?_complete$", .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="field_name", value="value") %>%
          dplyr::select_(.data=., .dots=intersect(variables_to_keep, colnames(.)))

        ds_2 <- ds %>%
          dplyr::mutate_if(is.character, type.convert) %>%
          dplyr::mutate_if(is.factor   , as.character)
      }, #Convert the raw text to a dataset.
      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 <- paste0(
        format(  nrow(ds), big.mark=",", scientific=FALSE, trim=TRUE), " records and ",
        format(length(ds), big.mark=",", scientific=FALSE, trim=TRUE), " columns were read from REDCap in ",
        round(kernel$elapsed_seconds, 1), " seconds.  The http status code was ", kernel$status_code, "."
      )

      kernel$raw_text   <- "" # If an operation is successful, the `raw_text` is no longer returned to save RAM.  The content is not really necessary with httr's status message exposed.
    } else {
      success           <- FALSE #Override the 'success' determination from the http status code.
      ds_2              <- tibble::tibble() #Return an empty data.frame
      outcome_message   <- paste0("The REDCap read failed.  The http status code was ", kernel$status_code, ".  The 'raw_text' returned was '", kernel$raw_text, "'.")
    }
  } else {
    ds_2            <- tibble::tibble() #Return an empty data.frame
    outcome_message <- if( any(grepl(kernel$regex_empty, kernel$raw_text)) ) {
      "The REDCapR read/export operation was not successful.  The returned dataset was empty."
    } else {
      paste0("The REDCapR read/export operation was not successful.  The error message was:\n",  kernel$raw_text)
    }
  }

  if( verbose )
    message(outcome_message)

  return( 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,
    events_collapsed   = events_collapsed,
    elapsed_seconds    = kernel$elapsed_seconds,
    raw_text           = kernel$raw_text
  ) )
}
OuhscBbmc/REDCapR documentation built on Aug. 15, 2018, 7:57 a.m.