specially: Perform a specialized validation with a user-defined function

In pointblank: Data Validation and Organization of Metadata for Local and Remote Tables

Perform a specialized validation with a user-defined function

Description

The specially() validation function allows for custom validation with a function that you provide. The major proviso for the provided function is that it must either return a logical vector or a table where the final column is logical. The function will operate on the table object, or, because you can do whatever you like, it could also operate on other types of objects. To do this, you can transform the input table in preconditions or inject an entirely different object there. During interrogation, there won't be any checks to ensure that the data is a table object.

Usage

specially(
  x,
  fn,
  preconditions = NULL,
  actions = NULL,
  step_id = NULL,
  label = NULL,
  brief = NULL,
  active = TRUE
)

expect_specially(object, fn, preconditions = NULL, threshold = 1)

test_specially(object, fn, preconditions = NULL, threshold = 1)

Arguments

x	A pointblank agent or a data table ⁠obj:<ptblank_agent>|obj:<tbl_*>⁠ // required A data frame, tibble (tbl_df or tbl_dbi), Spark DataFrame (tbl_spark), or, an agent object of class ptblank_agent that is commonly created with create_agent().
fn	Specialized validation function ⁠<function>⁠ // required A function that performs the specialized validation on the data. It must either return a logical vector or a table where the last column is a logical column.
preconditions	Input table modification prior to validation ⁠<table mutation expression>⁠ // default: NULL (optional) An optional expression for mutating the input table before proceeding with the validation. This can either be provided as a one-sided R formula using a leading ~ (e.g., ~ . %>% dplyr::mutate(col = col + 10) or as a function (e.g., function(x) dplyr::mutate(x, col = col + 10). See the Preconditions section for more information.
actions	Thresholds and actions for different states ⁠obj:<action_levels>⁠ // default: NULL (optional) A list containing threshold levels so that the validation step can react accordingly when exceeding the set levels for different states. This is to be created with the action_levels() helper function.
step_id	Manual setting of the step ID value ⁠scalar<character>⁠ // default: NULL (optional) One or more optional identifiers for the single or multiple validation steps generated from calling a validation function. The use of step IDs serves to distinguish validation steps from each other and provide an opportunity for supplying a more meaningful label compared to the step index. By default this is NULL, and pointblank will automatically generate the step ID value (based on the step index) in this case. One or more values can be provided, and the exact number of ID values should (1) match the number of validation steps that the validation function call will produce (influenced by the number of columns provided), (2) be an ID string not used in any previous validation step, and (3) be a vector with unique values.
label	Optional label for the validation step ⁠vector<character>⁠ // default: NULL (optional) Optional label for the validation step. This label appears in the agent report and, for the best appearance, it should be kept quite short. See the Labels section for more information.
brief	Brief description for the validation step ⁠scalar<character>⁠ // default: NULL (optional) A brief is a short, text-based description for the validation step. If nothing is provided here then an autobrief is generated by the agent, using the language provided in create_agent()'s lang argument (which defaults to "en" or English). The autobrief incorporates details of the validation step so it's often the preferred option in most cases (where a label might be better suited to succinctly describe the validation).
active	Is the validation step active? ⁠scalar<logical>⁠ // default: TRUE A logical value indicating whether the validation step should be active. If the validation function is working with an agent, FALSE will make the validation step inactive (still reporting its presence and keeping indexes for the steps unchanged). If the validation function will be operating directly on data (no agent involvement), then any step with active = FALSE will simply pass the data through with no validation whatsoever. Aside from a logical vector, a one-sided R formula using a leading ~ can be used with . (serving as the input data table) to evaluate to a single logical value. With this approach, the pointblank function has_columns() can be used to determine whether to make a validation step active on the basis of one or more columns existing in the table (e.g., ~ . %>% has_columns(c(d, e))).
object	A data table for expectations or tests ⁠obj:<tbl_*>⁠ // required A data frame, tibble (tbl_df or tbl_dbi), or Spark DataFrame (tbl_spark) that serves as the target table for the expectation function or the test function.
threshold	The failure threshold scalar<integer|numeric>(val>=0) // default: 1 A simple failure threshold value for use with the expectation (expect_) and the test (test_) function variants. By default, this is set to 1 meaning that any single unit of failure in data validation results in an overall test failure. Whole numbers beyond 1 indicate that any failing units up to that absolute threshold value will result in a succeeding testthat test or evaluate to TRUE. Likewise, fractional values (between 0 and 1) act as a proportional failure threshold, where 0.15 means that 15 percent of failing test units results in an overall test failure.

Value

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.

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).

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. Within specially(), because this function is special, there won't be internal checking as to whether the preconditions-based output is a table.

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)).

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).

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.

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.

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 specially() 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 specially() as a validation step is expressed in R code and in the corresponding YAML representation.

R statement:

agent %>% 
  specially(
    fn = function(x) { ... },
    preconditions = ~ . %>% dplyr::filter(a < 10),
    actions = action_levels(warn_at = 0.1, stop_at = 0.2), 
    label = "The `specially()` step.",
    active = FALSE
  )

YAML representation:

steps:
- specially:
    fn: function(x) { ... }
    preconditions: ~. %>% dplyr::filter(a < 10)
    actions:
      warn_fraction: 0.1
      stop_fraction: 0.2
    label: The `specially()` 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.

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.

tbl <-
  dplyr::tibble(
    a = c(5, 2, 6),
    b = c(3, 4, 6),
    c = c(9, 8, 7)
  )
  
tbl
#> # A tibble: 3 x 3
#>       a     b     c
#>   <dbl> <dbl> <dbl>
#> 1     5     3     9
#> 2     2     4     8
#> 3     6     6     7

A: Using an agent with validation functions and then interrogate()

Validate that the target table has exactly three rows. This single validation with specially() has 1 test unit since the function executed on x (the target table) results in a logical vector with a length of 1. We'll determine if this validation has any failing test units (there is 1 test unit).

agent <-
  create_agent(tbl = tbl) %>%
  specially(fn = function(x) nrow(x) == 3) %>%
  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.

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.

tbl %>% specially(fn = function(x) nrow(x) == 3)
#> # A tibble: 3 x 3
#>       a     b     c
#>   <dbl> <dbl> <dbl>
#> 1     5     3     9
#> 2     2     4     8
#> 3     6     6     7

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.

expect_specially(tbl, fn = function(x) nrow(x) == 3)

D: Using the test function

With the ⁠test_*()⁠ form, we should get a single logical value returned to us.

tbl %>% test_specially(fn = function(x) nrow(x) == 3)
#> [1] TRUE

Variations

We can do more complex things with specially() and its variants.

Check the class of the target table.

tbl %>% 
  test_specially(
    fn = function(x) {
      inherits(x, "data.frame")
    }
  )
#> [1] TRUE

Check that the number of rows in the target table is less than small_table.

tbl %>% 
  test_specially(
    fn = function(x) {
      nrow(x) < nrow(small_table)
    }
  )
#> [1] TRUE

Check that all numbers across all numeric column are less than 10.

tbl %>% 
  test_specially(
    fn = function(x) {
      (x %>% 
         dplyr::select(where(is.numeric)) %>%
         unlist()
      ) < 10
    }
  )
#> [1] TRUE

Check that all values in column c are greater than b and greater than a (in each row) and always less than 10. This creates a table with the new column d which is a logical column (that is used as the evaluation of test units).

tbl %>% 
  test_specially(
    fn = function(x) {
      x %>%
        dplyr::mutate(
          d = c > b & c > a & c < 10
        )
    }
  )
#> [1] TRUE

Check that the game_revenue table (which is not the target table) has exactly 2000 rows.

tbl %>% 
  test_specially(
    fn = function(x) {
      nrow(game_revenue) == 2000
    }
  )
#> [1] TRUE

Function ID

2-36

See Also

Other validation functions: col_count_match(), col_exists(), col_is_character(), col_is_date(), col_is_factor(), col_is_integer(), col_is_logical(), col_is_numeric(), col_is_posix(), col_schema_match(), col_vals_between(), col_vals_decreasing(), col_vals_equal(), col_vals_expr(), col_vals_gt(), col_vals_gte(), col_vals_in_set(), col_vals_increasing(), col_vals_lt(), col_vals_lte(), col_vals_make_set(), col_vals_make_subset(), col_vals_not_between(), col_vals_not_equal(), col_vals_not_in_set(), col_vals_not_null(), col_vals_null(), col_vals_regex(), col_vals_within_spec(), conjointly(), row_count_match(), rows_complete(), rows_distinct(), serially(), tbl_match()

pointblank documentation built on Oct. 30, 2024, 9:29 a.m.