inspectEHR: Data Quality Reporting for CC-HIC

#' #' XML Parsing Errors
#' #'
#' #' Interrogates and summarises XML parsing errors
#' #'
#' #' @param importstats uncollected importstats postGres table
#' #'
#' #' @return a tibble containing summary of XML errors
#' #' @export
#' #'
#' #' @examples
#' #' xml_stats(tbls[["importstats"]])
#' xml_stats <- function(importstats) {
#'   collect(importstats) %>%
#'     left_join(provenance %>%
#'       select(file_id, site), by = c("provenance_id" = "file_id")) %>%
#'     group_by(site) %>%
#'     summarise(
#'       episodes_read = sum(episodes_read),
#'       episodes_missing_key = sum(episodes_missing_key),
#'       events_dropped = sum(events_dropped)
#'     )
#' }
#'
#'
#'
#' #' Checks validation for XML files and returns a summary
#' #'
#' #' @param xml_file the xml file you wish to validate
#' #' @param schema the xml schema against which you are validating
#' #'
#' #' @return a character vector of linting errors
#' #' @export
#' #'
#' #' @importFrom xml2 read_xml xml_validate
#' #' @importFrom magrittr %>%
#' #' @importFrom stringr str_sub
#' #'
#' #' @examples
#' #' xml_validation(xml, schema)
#' xml_validation <- function(xml_file, schema) {
#'   xml_file_x <- xml2::read_xml(xml_file)
#'
#'   validation <- xml2::xml_validate(xml_file_x, schema)
#'
#'   if (validation == TRUE) {
#'     return(TRUE)
#'   } else {
#'     errors <- validation %>%
#'       base::attr(which = "errors") %>%
#'       stringr::str_sub(start = 54L, end = -1L)
#'
#'     return(errors)
#'   }
#' }
#'
#'
#' #' Summarise Event Level Errors
#' #'
#' #' returns a summary table grouped by site with a breakdown of the errors seen.
#' #' This is for overview purposes, so scope out the magnitude of problems and help
#' #' direct xml fixes
#' #'
#' #' @param errors error table
#' #' @param provenance provenance table
#' #'
#' #' @return a tibble with summary details of errors
#' #' @export
#' #'
#' #'
#' #' @examples
#' #' error_summary(xml_validation)
#' error_summary <- function(xml_validation) {
#'   xml_validation %>%
#'     dplyr::left_join(provenance %>% select(file_id, site), by = c("provenance_id" = "file_id")) %>%
#'     dplyr::mutate(message_type = dplyr::case_when(
#'       grepl("clock change", message) ~ "Daylight saving bug",
#'       grepl("nhs number", message) ~ "Missing NHS Number",
#'       grepl("empty tags|Empty tags", message) ~ "Empty XML Tags",
#'       grepl("primary value", message) ~ "Missing Primary Value",
#'       grepl("Rejected patient", message) ~ "Patient Rejected (Other)",
#'       grepl("integer value is out of range", message) ~ "Numeric Out of Range",
#'       grepl("Got float, expected int", message) ~ "Wrong Data Type",
#'       grepl("not a valid value of the atomic type \'xs:integer\'", message) ~ "Wrong Data Type",
#'       grepl("could not convert string to float", message) ~ "Wrong Data Type",
#'       grepl("is not an element of the set", message) ~ "Wrong Data Type",
#'       TRUE ~ "Other"
#'     )) %>%
#'     dplyr::group_by(site, message_type) %>%
#'     dplyr::summarise(count = n())
#' }