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serially.R
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serially.R
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#------------------------------------------------------------------------------#
#
# _ _ _ _ _
# (_) | | | | | | | |
# _ __ ___ _ _ __ | |_ | |__ | | __ _ _ __ | | __
# | '_ \ / _ \ | || '_ \ | __|| '_ \ | | / _` || '_ \ | |/ /
# | |_) || (_) || || | | || |_ | |_) || || (_| || | | || <
# | .__/ \___/ |_||_| |_| \__||_.__/ |_| \__,_||_| |_||_|\_\
# | |
# |_|
#
# This file is part of the 'rstudio/pointblank' project.
#
# Copyright (c) 2017-2024 pointblank authors
#
# For full copyright and license information, please look at
# https://rstudio.github.io/pointblank/LICENSE.html
#
#------------------------------------------------------------------------------#
#' Run several tests and a final validation in a serial manner
#'
#' @description
#'
#' The `serially()` validation function allows for a series of tests to run in
#' sequence before either culminating in a final validation step or simply
#' exiting the series. This construction allows for pre-testing that may make
#' sense before a validation step. For example, there may be situations where
#' it's vital to check a column type before performing a validation on the same
#' column (since having the wrong type can result in an evaluation error for the
#' subsequent validation). Another serial workflow might entail having a bundle
#' of checks in a prescribed order and, if all pass, then the goal of this
#' testing has been achieved (e.g., checking if a table matches another through
#' a series of increasingly specific tests).
#'
#' A series as specified inside `serially()` is composed with a listing of
#' calls, and we would draw upon test functions (**T**) to describe tests and
#' optionally provide a finalizing call with a validation function (**V**).
#' The following constraints apply:
#'
#' - there must be at least one test function in the series (**T** -> **V** is
#' good, **V** is *not*)
#' - there can only be one validation function call, **V**; it's optional but,
#' if included, it must be placed at the end (**T** -> **T** -> **V** is good,
#' these sequences are bad: (1) **T** -> **V** -> **T**, (2) **T** -> **T** ->
#' **V** -> **V**)
#' - a validation function call (**V**), if included, mustn't itself yield
#' multiple validation steps (this may happen when providing multiple `columns`
#' or any `segments`)
#'
#' Here's an example of how to arrange expressions:
#'
#' ```
#' ~ test_col_exists(., columns = count),
#' ~ test_col_is_numeric(., columns = count),
#' ~ col_vals_gt(., columns = count, value = 2)
#' ```
#'
#' This series concentrates on the column called `count` and first checks
#' whether the column exists, then checks if that column is numeric, and then
#' finally validates whether all values in the column are greater than `2`.
#'
#' Note that in the above listing of calls, the `.` stands in for the target
#' table and is always necessary here. Also important is that all `test_*()`
#' functions have a `threshold` argument that is set to `1` by default. Should
#' you need to bump up the threshold value it can be changed to a different
#' integer value (as an absolute threshold of failing test units) or a
#' decimal value between `0` and `1` (serving as a fractional threshold of
#' failing test units).
#'
#' @inheritParams col_vals_gt
#'
#' @param ... *Test/validation expressions*
#'
#' `<test/validation expressions>` // **required** (or, use `.list`)
#'
#' A collection one-sided formulas that consist of `test_*()` function calls
#' (e.g., [test_col_vals_between()], etc.) arranged in sequence of intended
#' interrogation order. Typically, validations up until the final one would
#' have some `threshold` value set (default is `1`) for short circuiting
#' within the series. A finishing validation function call (e.g.,
#' [col_vals_increasing()], etc.) can optionally be inserted at the end of the
#' series, serving as a validation step that only undergoes interrogation if
#' the prior tests adequately pass. An example of this is
#' `~ test_column_exists(., a), ~ col_vals_not_null(., a)`).
#'
#' @param .list *Alternative to `...`*
#'
#' `<list of multiple expressions>` // **required** (or, use `...`)
#'
#' Allows for the use of a list as an input alternative to `...`.
#'
#' @return For the validation function, the return value is either a
#' `ptblank_agent` object or a table object (depending on whether an agent
#' object or a table was passed to `x`). The expectation function invisibly
#' returns its input but, in the context of testing data, the function is
#' called primarily for its potential side-effects (e.g., signaling failure).
#' The test function returns a logical value.
#'
#' @section Supported Input Tables:
#'
#' The types of data tables that are officially supported are:
#'
#' - data frames (`data.frame`) and tibbles (`tbl_df`)
#' - Spark DataFrames (`tbl_spark`)
#' - the following database tables (`tbl_dbi`):
#' - *PostgreSQL* tables (using the `RPostgres::Postgres()` as driver)
#' - *MySQL* tables (with `RMySQL::MySQL()`)
#' - *Microsoft SQL Server* tables (via **odbc**)
#' - *BigQuery* tables (using `bigrquery::bigquery()`)
#' - *DuckDB* tables (through `duckdb::duckdb()`)
#' - *SQLite* (with `RSQLite::SQLite()`)
#'
#' Other database tables may work to varying degrees but they haven't been
#' formally tested (so be mindful of this when using unsupported backends with
#' **pointblank**).
#'
#' @section Column Names:
#'
#' `columns` may be a single column (as symbol `a` or string `"a"`) or a vector
#' of columns (`c(a, b, c)` or `c("a", "b", "c")`). `{tidyselect}` helpers
#' are also supported, such as `contains("date")` and `where(is.double)`. If
#' passing an *external vector* of columns, it should be wrapped in `all_of()`.
#'
#' When multiple columns are selected by `columns`, the result will be an
#' expansion of validation steps to that number of columns (e.g.,
#' `c(col_a, col_b)` will result in the entry of two validation steps).
#'
#' Previously, columns could be specified in `vars()`. This continues to work,
#' but `c()` offers the same capability and supersedes `vars()` in `columns`.
#'
#' @section Preconditions:
#'
#' Providing expressions as `preconditions` means **pointblank** will preprocess
#' the target table during interrogation as a preparatory step. It might happen
#' that a particular validation requires a calculated column, some filtering of
#' rows, or the addition of columns via a join, etc. Especially for an
#' *agent*-based report this can be advantageous since we can develop a large
#' validation plan with a single target table and make minor adjustments to it,
#' as needed, along the way.
#'
#' The table mutation is totally isolated in scope to the validation step(s)
#' where `preconditions` is used. Using **dplyr** code is suggested here since
#' the statements can be translated to SQL if necessary (i.e., if the target
#' table resides in a database). The code is most easily supplied as a one-sided
#' **R** formula (using a leading `~`). In the formula representation, the `.`
#' serves as the input data table to be transformed (e.g., `~ . %>%
#' dplyr::mutate(col_b = col_a + 10)`). Alternatively, a function could instead
#' be supplied (e.g., `function(x) dplyr::mutate(x, col_b = col_a + 10)`).
#'
#' @section Actions:
#'
#' Often, we will want to specify `actions` for the validation. This argument,
#' present in every validation function, takes a specially-crafted list
#' object that is best produced by the [action_levels()] function. Read that
#' function's documentation for the lowdown on how to create reactions to
#' above-threshold failure levels in validation. The basic gist is that you'll
#' want at least a single threshold level (specified as either the fraction of
#' test units failed, or, an absolute value), often using the `warn_at`
#' argument. This is especially true when `x` is a table object because,
#' otherwise, nothing happens. For the `col_vals_*()`-type functions, using
#' `action_levels(warn_at = 0.25)` or `action_levels(stop_at = 0.25)` are good
#' choices depending on the situation (the first produces a warning when a
#' quarter of the total test units fails, the other `stop()`s at the same
#' threshold level).
#'
#' @section Labels:
#'
#' `label` may be a single string or a character vector that matches the number
#' of expanded steps. `label` also supports `{glue}` syntax and exposes the
#' following dynamic variables contextualized to the current step:
#'
#' - `"{.step}"`: The validation step name
#'
#' The glue context also supports ordinary expressions for further flexibility
#' (e.g., `"{toupper(.step)}"`) as long as they return a length-1 string.
#'
#' @section Briefs:
#'
#' Want to describe this validation step in some detail? Keep in mind that this
#' is only useful if `x` is an *agent*. If that's the case, `brief` the agent
#' with some text that fits. Don't worry if you don't want to do it. The
#' *autobrief* protocol is kicked in when `brief = NULL` and a simple brief will
#' then be automatically generated.
#'
#' @section YAML:
#'
#' A **pointblank** agent can be written to YAML with [yaml_write()] and the
#' resulting YAML can be used to regenerate an agent (with [yaml_read_agent()])
#' or interrogate the target table (via [yaml_agent_interrogate()]). When
#' `serially()` is represented in YAML (under the top-level `steps` key as a
#' list member), the syntax closely follows the signature of the validation
#' function. Here is an example of how a complex call of `serially()` as a
#' validation step is expressed in R code and in the corresponding YAML
#' representation.
#'
#' R statement:
#'
#' ```r
#' agent %>%
#' serially(
#' ~ test_col_vals_lt(., columns = a, value = 8),
#' ~ test_col_vals_gt(., columns = c, value = vars(a)),
#' ~ col_vals_not_null(., columns = b),
#' preconditions = ~ . %>% dplyr::filter(a < 10),
#' actions = action_levels(warn_at = 0.1, stop_at = 0.2),
#' label = "The `serially()` step.",
#' active = FALSE
#' )
#' ```
#'
#' YAML representation:
#'
#' ```yaml
#' steps:
#' - serially:
#' fns:
#' - ~test_col_vals_lt(., columns = a, value = 8)
#' - ~test_col_vals_gt(., columns = c, value = vars(a))
#' - ~col_vals_not_null(., columns = b)
#' preconditions: ~. %>% dplyr::filter(a < 10)
#' actions:
#' warn_fraction: 0.1
#' stop_fraction: 0.2
#' label: The `serially()` step.
#' active: false
#' ```
#'
#' In practice, both of these will often be shorter as only the expressions for
#' validation steps are necessary. Arguments with default values won't be
#' written to YAML when using [yaml_write()] (though it is acceptable to include
#' them with their default when generating the YAML by other means). It is also
#' possible to preview the transformation of an agent to YAML without any
#' writing to disk by using the [yaml_agent_string()] function.
#'
#' @section Examples:
#'
#' For all examples here, we'll use a simple table with three numeric columns
#' (`a`, `b`, and `c`). This is a very basic table but it'll be more useful when
#' explaining things later.
#'
#' ```{r}
#' tbl <-
#' dplyr::tibble(
#' a = c(5, 2, 6),
#' b = c(6, 4, 9),
#' c = c(1, 2, 3)
#' )
#'
#' tbl
#' ```
#'
#' ## A: Using an `agent` with validation functions and then `interrogate()`
#'
#' The `serially()` function can be set up to perform a series of tests and then
#' perform a validation (only if all tests pass). Here, we are going to (1) test
#' whether columns `a` and `b` are numeric, (2) check that both don't have any
#' `NA` values, and (3) perform a finalizing validation that checks whether
#' values in `b` are greater than values in `a`. We'll determine if this
#' validation has any failing test units (there are 4 tests and a final
#' validation).
#'
#' ```r
#' agent_1 <-
#' create_agent(tbl = tbl) %>%
#' serially(
#' ~ test_col_is_numeric(., columns = c(a, b)),
#' ~ test_col_vals_not_null(., columns = c(a, b)),
#' ~ col_vals_gt(., columns = b, value = vars(a))
#' ) %>%
#' interrogate()
#' ```
#'
#' Printing the `agent` in the console shows the validation report in the
#' Viewer. Here is an excerpt of validation report, showing the single entry
#' that corresponds to the validation step demonstrated here.
#'
#' \if{html}{
#' \out{
#' `r pb_get_image_tag(file = "man_serially_1.png")`
#' }
#' }
#'
#' What's going on? All four of the tests passed and so the final validation
#' occurred. There were no failing test units in that either!
#'
#' The final validation is optional and so here is a variation where only the
#' serial tests are performed.
#'
#' ```r
#' agent_2 <-
#' create_agent(tbl = tbl) %>%
#' serially(
#' ~ test_col_is_numeric(., columns = c(a, b)),
#' ~ test_col_vals_not_null(., columns = c(a, b))
#' ) %>%
#' interrogate()
#' ```
#'
#' Everything is good here too:
#'
#' \if{html}{
#' \out{
#' `r pb_get_image_tag(file = "man_serially_2.png")`
#' }
#' }
#'
#' ## B: Using the validation function directly on the data (no `agent`)
#'
#' This way of using validation functions acts as a data filter. Data is passed
#' through but should `stop()` if there is a single test unit failing. The
#' behavior of side effects can be customized with the `actions` option.
#'
#' ```{r}
#' tbl %>%
#' serially(
#' ~ test_col_is_numeric(., columns = c(a, b)),
#' ~ test_col_vals_not_null(., columns = c(a, b)),
#' ~ col_vals_gt(., columns = b, value = vars(a))
#' )
#' ```
#'
#' ## C: Using the expectation function
#'
#' With the `expect_*()` form, we would typically perform one validation at a
#' time. This is primarily used in **testthat** tests.
#'
#' ```r
#' expect_serially(
#' tbl,
#' ~ test_col_is_numeric(., columns = c(a, b)),
#' ~ test_col_vals_not_null(., columns = c(a, b)),
#' ~ col_vals_gt(., columns = b, value = vars(a))
#' )
#' ```
#'
#' ## D: Using the test function
#'
#' With the `test_*()` form, we should get a single logical value returned to
#' us.
#'
#' ```{r}
#' tbl %>%
#' test_serially(
#' ~ test_col_is_numeric(., columns = c(a, b)),
#' ~ test_col_vals_not_null(., columns = c(a, b)),
#' ~ col_vals_gt(., columns = b, value = vars(a))
#' )
#' ```
#'
#' @family validation functions
#' @section Function ID:
#' 2-35
#'
#' @name serially
NULL
#' @rdname serially
#' @import rlang
#'
#' @export
serially <- function(
x,
...,
.list = list2(...),
preconditions = NULL,
actions = NULL,
step_id = NULL,
label = NULL,
brief = NULL,
active = TRUE
) {
segments <- NULL
# Obtain all of the group's elements
list_elements <- .list
dots_attrs <- list_elements[rlang::names2(list_elements) != ""]
validation_formulas <-
list_elements[
vapply(
list_elements,
function(x) rlang::is_formula(x),
FUN.VALUE = logical(1),
USE.NAMES = FALSE
)
]
assertion_types <-
vapply(
validation_formulas,
FUN.VALUE = character(1),
USE.NAMES = FALSE,
FUN = function(x) {
x %>%
rlang::f_rhs() %>%
as.character() %>%
.[[1]]
}
)
# Check that the vector of `assertion_types` uses valid
# validation function names (including the `test_*()` variants)
in_set_of_fns <-
all(
assertion_types %in%
c(
all_validations_fns_vec(),
paste0("test_", all_validations_fns_vec())
)
)
if (!in_set_of_fns) {
stop(
"All `serially()` steps must use validation or test function calls.",
call. = FALSE
)
}
# There must be at least one `test_*()` step; if not, stop the function
has_a_test <-
any(assertion_types %in% paste0("test_", all_validations_fns_vec()))
if (!has_a_test) {
stop(
"There must be at least one `test_*()` function call in `serially()`.",
call. = FALSE
)
}
# Check whether the series has any validation calls
any_validations <-
any(assertion_types %in% all_validations_fns_vec())
# If there are any validations we must ensure a few things
# [1] there isn't more than one call
# [2] the validation call must be the final call
# [3] the finalizing validation mustn't itself yield multiple steps
if (any_validations) {
# Check [1]: more than one validation function call
has_multiple_validations <-
sum(assertion_types %in% all_validations_fns_vec()) > 1
if (has_multiple_validations) {
stop(
"There cannot be multiple validation function calls in `serially()`",
call. = FALSE
)
}
# Check [2]: validation function call must be final call
validation_is_final_call <-
which(assertion_types %in% all_validations_fns_vec()) ==
length(assertion_types)
if (!validation_is_final_call) {
stop(
"The validation function call must be the final one in `serially()`",
call. = FALSE
)
}
# Check [3]: the validation function call cannot yield multiple steps
validation_step_call_args <-
validation_formulas[length(validation_formulas)][[1]] %>%
as.call() %>%
rlang::call_args()
# Check the first argument
if (!as.character(validation_step_call_args[[1]]) == ".") {
stop(
"The first argument to a validation function call must be \".\"",
call. = FALSE
)
}
# Check whether the validation function is of type that has an
# expandable `columns` argument
has_expandable_cols_arg <-
assertion_types[length(assertion_types)] %in%
base::setdiff(
all_validations_fns_vec(),
c(
"rows_distinct", "rows_complete",
"col_vals_expr", "col_schema_match",
"conjointly"
)
)
if (has_expandable_cols_arg) {
has_multiple_cols <-
rlang::as_label(validation_step_call_args[[2]]) %>%
gsub("^\"|\"$", "", .) %>%
grepl(",", x = .)
if (has_multiple_cols) {
stop(
"The finalizing validation function call must only operate on a ",
"single column",
call. = FALSE
)
}
}
}
# Resolve segments into list
segments_list <-
resolve_segments(
x = x,
seg_expr = segments,
preconditions = preconditions
)
if (is_a_table_object(x)) {
secret_agent <-
create_agent(x, label = "::QUIET::") %>%
serially(
.list = .list,
preconditions = preconditions,
segments = segments,
actions = prime_actions(actions),
label = label,
brief = brief,
active = active
) %>%
interrogate()
return(x)
}
agent <- x
if (is.null(brief)) {
validation_n <- length(validation_formulas)
assertion_types <-
vapply(
validation_formulas,
FUN.VALUE = character(1),
USE.NAMES = FALSE,
FUN = function(x) {
x %>%
rlang::f_rhs() %>%
as.character() %>%
.[[1]]
}
)
# Initialize the `serially_validation_set` tibble
serially_validation_set <- dplyr::tibble()
has_final_validation <-
assertion_types[length(assertion_types)] %in% all_validations_fns_vec()
# Get the total number of `test_*()` calls supplied
test_call_n <-
if (has_final_validation) validation_n - 1 else validation_n
#
# Determine the total number of test steps
#
# Create a `double_agent` that will be used just for determining
# the number of test steps
double_agent <- create_agent(tbl = dplyr::tibble(), label = "::QUIET::")
for (k in seq_len(test_call_n)) {
double_agent <-
eval(
expr = parse(
text =
validation_formulas[[k]] %>%
rlang::f_rhs() %>%
rlang::expr_deparse() %>%
tidy_gsub("(.", "(double_agent", fixed = TRUE) %>%
tidy_gsub("^test_", "") %>%
tidy_gsub("threshold\\s+?=\\s.*$", ")") %>%
tidy_gsub(",\\s+?\\)$", ")")
),
envir = NULL
)
}
test_step_n <- nrow(double_agent$validation_set)
if (has_final_validation) {
final_validation_type <- assertion_types[length(assertion_types)]
double_agent <- create_agent(tbl = dplyr::tibble(), label = "::QUIET::")
double_agent <-
eval(
expr = parse(
text =
validation_formulas[[length(validation_formulas)]] %>%
rlang::f_rhs() %>%
rlang::expr_deparse() %>%
tidy_gsub("(.", "(double_agent", fixed = TRUE) %>%
tidy_gsub("^test_", "") %>%
tidy_gsub("threshold\\s+?=\\s.*$", ")") %>%
tidy_gsub(",\\s+?\\)$", ")")
),
envir = NULL
)
final_validation_values <- double_agent$validation_set$values
final_validation_column <- double_agent$validation_set$column
} else {
final_validation_type <- NA_character_
final_validation_values <- list(NULL)
final_validation_column <- list(NULL)
}
brief <-
create_autobrief(
agent = agent,
assertion_type = "serially",
preconditions = preconditions,
values = list(
validation_formulas = validation_formulas,
total_test_calls = test_call_n,
total_test_steps = test_step_n,
has_final_validation = has_final_validation,
final_validation_type = final_validation_type,
final_validation_column = final_validation_column,
final_validation_values = final_validation_values
)
)
}
# Normalize any provided `step_id` value(s)
step_id <- normalize_step_id(step_id, columns = "column", agent)
# Get the next step number for the `validation_set` tibble
i_o <- get_next_validation_set_row(agent)
# Check `step_id` value(s) against all other `step_id`
# values in earlier validation steps
check_step_id_duplicates(step_id, agent)
# Add one or more validation steps based on the
# length of `segments_list`
label <- resolve_label(label, segments = segments_list)
for (i in seq_along(segments_list)) {
seg_col <- names(segments_list[i])
seg_val <- unname(unlist(segments_list[i]))
agent <-
create_validation_step(
agent = agent,
assertion_type = "serially",
i_o = i_o,
columns_expr = NULL,
column = NULL,
values = validation_formulas,
na_pass = NULL,
preconditions = preconditions,
seg_expr = segments,
seg_col = seg_col,
seg_val = seg_val,
actions = covert_actions(actions, agent),
step_id = step_id,
label = label[[i]],
brief = brief,
active = active
)
}
agent
}
#' @rdname serially
#' @import rlang
#' @export
expect_serially <- function(
object,
...,
.list = list2(...),
preconditions = NULL,
threshold = 1
) {
fn_name <- "expect_serially"
vs <-
create_agent(tbl = object, label = "::QUIET::") %>%
serially(
.list = .list,
preconditions = {{ preconditions }},
actions = action_levels(notify_at = threshold)
) %>%
interrogate() %>%
.$validation_set
x <- vs$notify %>% all()
threshold_type <- get_threshold_type(threshold = threshold)
if (threshold_type == "proportional") {
failed_amount <- vs$f_failed
} else {
failed_amount <- vs$n_failed
}
# TODO: express warnings and errors here
act <- testthat::quasi_label(enquo(x), arg = "object")
values_text <- prep_values_text(values = vs$values, limit = 3, lang = "en")
testthat::expect(
ok = identical(!as.vector(act$val), TRUE),
failure_message = glue::glue(
failure_message_gluestring(
fn_name = fn_name, lang = "en"
)
)
)
act$val <- object
invisible(act$val)
}
#' @rdname serially
#' @import rlang
#' @export
test_serially <- function(
object,
...,
.list = list2(...),
preconditions = NULL,
threshold = 1
) {
vs <-
create_agent(tbl = object, label = "::QUIET::") %>%
serially(
.list = .list,
preconditions = {{ preconditions }},
actions = action_levels(notify_at = threshold)
) %>%
interrogate() %>%
.$validation_set
if (inherits(vs$capture_stack[[1]]$warning, "simpleWarning")) {
warning(conditionMessage(vs$capture_stack[[1]]$warning))
}
if (inherits(vs$capture_stack[[1]]$error, "simpleError")) {
stop(conditionMessage(vs$capture_stack[[1]]$error))
}
all(!vs$notify)
}