mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 01:49:39 +02:00
390 lines
9.6 KiB
R
390 lines
9.6 KiB
R
# Description of warning with text description incl metric
|
|
# Color coded (green (OK) or yellow (WARNING))
|
|
# option to ignore/accept warnings ### to simplify things, this is gone for now ###
|
|
# Only show warnings based on performed analyses
|
|
|
|
## 250825
|
|
## Works in demo
|
|
## Not alert is printed in app interface
|
|
## I believe it comes down to the reactivity
|
|
|
|
|
|
########################################################################
|
|
############# Server and UI
|
|
########################################################################
|
|
|
|
#' @title Validation module
|
|
#'
|
|
#' @description Check that a dataset respect some validation expectations.
|
|
#'
|
|
#' @param id Module's ID.
|
|
#' @param max_height Maximum height for validation results element, useful if you have many rules.
|
|
#' @param ... Arguments passed to \code{actionButton} or \code{uiOutput} depending on display mode,
|
|
#' you cannot use \code{inputId}/\code{outputId}, \code{label} or \code{icon} (button only).
|
|
#'
|
|
#' @return
|
|
#' * UI: HTML tags that can be included in shiny's UI
|
|
#' * Server: a \code{list} with two slots:
|
|
#' + **status**: a \code{reactive} function returning the best status available between \code{"OK"}, \code{"Failed"} or \code{"Error"}.
|
|
#' + **details**: a \code{reactive} function returning a \code{list} with validation details.
|
|
#' @export
|
|
#'
|
|
#' @rdname validation
|
|
#'
|
|
#' @example examples/validation_module_demo.R
|
|
validation_ui <- function(id, max_height = NULL, ...) {
|
|
ns <- shiny::NS(id)
|
|
|
|
max_height <- if (!is.null(max_height)) {
|
|
paste0("overflow-y: auto; max-height:", htmltools::validateCssUnit(max_height), ";")
|
|
}
|
|
|
|
ui <- shiny::uiOutput(
|
|
outputId = ns("results"),
|
|
...,
|
|
style = max_height
|
|
)
|
|
|
|
htmltools::tagList(
|
|
ui, datamods:::html_dependency_datamods()
|
|
)
|
|
}
|
|
|
|
#' @export
|
|
#'
|
|
#' @param data a \code{reactive} function returning a \code{data.frame}.
|
|
#'
|
|
#' @rdname validation
|
|
#'
|
|
validation_server <- function(id,
|
|
data) {
|
|
moduleServer(
|
|
id = id,
|
|
module = function(input, output, session) {
|
|
valid_ui <- reactiveValues(x = NULL)
|
|
|
|
data_r <- if (shiny::is.reactive(data)) data else shiny::reactive(data)
|
|
|
|
# observeEvent(data_r(), {
|
|
# to_validate <- data()
|
|
# valid_dims <- check_data(to_validate, n_row = n_row, n_col = n_col)
|
|
#
|
|
# if (all(c(valid_dims$nrows, valid_dims$ncols))) {
|
|
# valid_status <- "OK"
|
|
# } else {
|
|
# valid_status <- "Failed"
|
|
# }
|
|
#
|
|
# valid_results <- lapply(
|
|
# X = c("nrows", "ncols"),
|
|
# FUN = function(x) {
|
|
# if (is.null(valid_dims[[x]]))
|
|
# return(NULL)
|
|
# label <- switch(
|
|
# x,
|
|
# "nrows" = n_row_label,
|
|
# "ncols" = n_col_label
|
|
# )
|
|
# list(
|
|
# status = ifelse(valid_dims[[x]], "OK", "Failed"),
|
|
# label = paste0("<b>", label, "</b>")
|
|
# )
|
|
# }
|
|
# )
|
|
|
|
shiny::observeEvent(
|
|
data_r(),
|
|
{
|
|
# browser()
|
|
to_validate <- data_r()
|
|
if (is.reactivevalues(to_validate))
|
|
out <- lapply(
|
|
reactiveValuesToList(to_validate),
|
|
make_validation_alerts) |>
|
|
purrr::list_flatten()
|
|
|
|
if (length(to_validate) > 0) {
|
|
out <- make_validation_alerts(to_validate)
|
|
}
|
|
valid_ui$x <- tagList(out)
|
|
}
|
|
)
|
|
|
|
output$results <- renderUI({
|
|
valid_ui$x
|
|
})
|
|
}
|
|
)
|
|
}
|
|
|
|
|
|
########################################################################
|
|
############# Validation functions
|
|
########################################################################
|
|
|
|
#' Dimensions validation
|
|
#'
|
|
#' @param before data before
|
|
#' @param after data after
|
|
#' @param fun dimension function. ncol or nrow
|
|
#'
|
|
#' @returns data.frame
|
|
#'
|
|
dim_change_call <- function(before, after, fun) {
|
|
# browser()
|
|
if (!0 %in% c(dim(before), dim(after))) {
|
|
n_before <- fun(before)
|
|
n_after <- fun(after)
|
|
n_out <- n_before - n_after
|
|
p_after <- n_after / fun(before) * 100
|
|
p_out <- 100 - p_after
|
|
|
|
data.frame(
|
|
n_before = n_before,
|
|
n_after = n_after,
|
|
n_out = n_out,
|
|
p_after = p_after,
|
|
p_out = p_out
|
|
) |>
|
|
dplyr::mutate(
|
|
dplyr::across(
|
|
dplyr::where(
|
|
is.numeric
|
|
),
|
|
\(.y) round(.y, 0)
|
|
)
|
|
)
|
|
} else {
|
|
data.frame(NULL)
|
|
}
|
|
}
|
|
|
|
#' Variable filter test wrapper
|
|
#'
|
|
#' @param before data before
|
|
#' @param after data after
|
|
#'
|
|
#' @returns vector
|
|
#'
|
|
#' @examples
|
|
#' vars_filter_validate(mtcars, mtcars[1:6])
|
|
#' vars_filter_validate(mtcars, mtcars[0])
|
|
vars_filter_validate <- function(before, after) {
|
|
dim_change_call(before, after, ncol)
|
|
}
|
|
|
|
#' Observations filter test wrapper
|
|
#'
|
|
#' @param before data before
|
|
#' @param after data after
|
|
#'
|
|
#' @returns vector
|
|
#'
|
|
obs_filter_validate <- function(before, after) {
|
|
dim_change_call(before, after, nrow)
|
|
}
|
|
|
|
#' Validate function of missingness in data
|
|
#'
|
|
#' @param data data set
|
|
#'
|
|
#' @returns data.frame
|
|
#' @export
|
|
#'
|
|
#' @examples
|
|
#' df <- mtcars
|
|
#' df[1,2:4] <- NA
|
|
#' missings_validate(df)
|
|
missings_validate <- function(data){
|
|
if (!0 %in% dim(data)) {
|
|
# browser()
|
|
p_miss <- sum(is.na(data))/prod(dim(data))*100
|
|
data.frame(
|
|
p_miss = p_miss
|
|
) |>
|
|
dplyr::mutate(
|
|
dplyr::across(
|
|
dplyr::where(
|
|
is.numeric
|
|
),
|
|
\(.y) signif(.y, 2)
|
|
)
|
|
)
|
|
} else {
|
|
data.frame(NULL)
|
|
}
|
|
}
|
|
|
|
|
|
########################################################################
|
|
############# Collected validation functions in a library-like function
|
|
########################################################################
|
|
|
|
|
|
#' Validation library
|
|
#'
|
|
#' @param name Index name
|
|
#'
|
|
#' @returns list
|
|
#'
|
|
#' @examples
|
|
#' validation_lib()
|
|
#' validation_lib("missings")
|
|
validation_lib <- function(name=NULL) {
|
|
ls <- list(
|
|
"obs_filter" = function(x, y) {
|
|
## Validation function for observations filter
|
|
list(
|
|
string = i18n$t("You removed {p_out} % of observations."),
|
|
summary.fun = obs_filter_validate,
|
|
summary.fun.args = list(
|
|
before = x,
|
|
after = y
|
|
),
|
|
test.fun = function(x, var, cut) {
|
|
test.var <- x[var]
|
|
ifelse(test.var > cut, "warning", "succes")
|
|
},
|
|
test.fun.args = list(var = "p_out", cut = 50)
|
|
)
|
|
},
|
|
"var_filter" = function(x, y) {
|
|
## Validation function for variables filter
|
|
list(
|
|
string = i18n$t("You removed {p_out} % of variables."),
|
|
summary.fun = vars_filter_validate,
|
|
summary.fun.args = list(
|
|
before = x,
|
|
after = y
|
|
),
|
|
test.fun = function(x, var, cut) {
|
|
test.var <- x[var]
|
|
ifelse(test.var > cut, "warning", "succes")
|
|
},
|
|
test.fun.args = list(var = "p_out", cut = 50)
|
|
)
|
|
},
|
|
"missings" = function(x, y) {
|
|
### Placeholder for missingness validation
|
|
list(
|
|
string = "There are {p_miss} % missing observations.",
|
|
summary.fun = missings_validate,
|
|
summary.fun.args = list(
|
|
data = x
|
|
),
|
|
test.fun = function(x, var, cut) {
|
|
test.var <- x[var]
|
|
ifelse(test.var > cut, "warning", "succes")
|
|
},
|
|
test.fun.args = list(var = "p_miss", cut = 30)
|
|
)
|
|
}
|
|
)
|
|
|
|
if (!is.null(name)){
|
|
name <- match.arg(name,choices = names(ls))
|
|
ls[[name]]
|
|
} else {
|
|
ls
|
|
}
|
|
}
|
|
|
|
|
|
########################################################################
|
|
############# Validation creation
|
|
########################################################################
|
|
|
|
#' Create validation data.frame
|
|
#'
|
|
#' @param ls validation list
|
|
#' @param ... magic dots
|
|
#'
|
|
#' @returns data.frame
|
|
#' @export
|
|
#'
|
|
#' @examples
|
|
#' i18n <- shiny.i18n::Translator$new(translation_csvs_path = here::here("inst/translations"))
|
|
#' i18n$set_translation_language("en")
|
|
#' df_original <- mtcars
|
|
#' df_original[1,2:4] <- NA
|
|
#' df_obs <- df_original |> dplyr::filter(carb==4)
|
|
#' df_vars <- df_original[1:7]
|
|
#' val <- purrr::map2(
|
|
#' .x = validation_lib(),
|
|
#' .y = list(
|
|
#' list(x = df_original, y = df_obs),
|
|
#' list(x = df_original, y = df_vars),
|
|
#' list(x=df_original)),
|
|
#' make_validation
|
|
#' )
|
|
#' val |> make_validation_alerts()
|
|
#'
|
|
#' val2 <- purrr::map2(
|
|
#' .x = validation_lib()[2],
|
|
#' .y = list(list(x = mtcars, y = mtcars[0])),
|
|
#' make_validation
|
|
#' )
|
|
#' val2 |> make_validation_alerts()
|
|
#'
|
|
#' val3 <- make_validation(
|
|
#' ls = validation_lib()[[2]],
|
|
#' list(x = mtcars, y = mtcars[0])
|
|
#' )
|
|
make_validation <- function(ls, ...) {
|
|
ls <- do.call(ls, ...)
|
|
|
|
df <- do.call(ls$summary.fun, ls$summary.fun.args)
|
|
|
|
if (!any(dim(df) == c(0))) {
|
|
label <- with(df, {
|
|
glue::glue(ls$string)
|
|
})
|
|
|
|
# browser()
|
|
status <- do.call(ls$test.fun, modifyList(ls$test.fun.args, list(x = df)))
|
|
|
|
data.frame(
|
|
label = label,
|
|
status = status[1]
|
|
)
|
|
} else {
|
|
data.frame(NULL)
|
|
}
|
|
}
|
|
|
|
|
|
#' Create alert from validation data.frame
|
|
#'
|
|
#' @param data
|
|
#'
|
|
#' @export
|
|
make_validation_alerts <- function(data) {
|
|
# browser()
|
|
if (is.data.frame(data)){
|
|
ls <- list(data)
|
|
} else {
|
|
ls <- data
|
|
}
|
|
|
|
lapply(
|
|
X = ls,
|
|
FUN = function(x) {
|
|
# browser()
|
|
if (!is.null(dim(x)) && !any(dim(x) == c(0))) {
|
|
icon <- switch(x$status,
|
|
"succes" = phosphoricons::ph("check", title = "OK"),
|
|
"warning" = phosphoricons::ph("warning", title = "Warning")
|
|
)
|
|
|
|
shinyWidgets::alert(
|
|
icon,
|
|
htmltools::HTML(x$label),
|
|
status = x$status,
|
|
style = "margin-bottom: 10px; padding: 10px;"
|
|
)
|
|
} else {
|
|
return(NULL)
|
|
}
|
|
}
|
|
)
|
|
}
|