write_testthat_file: Transform a *pointblank* agent to a *testthat* test file

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

Transform a pointblank agent to a testthat test file

Description

With a pointblank agent, we can write a testthat test file and opt to place it in the testthat/tests if it is available in the project path (we can specify an alternate path as well). This works by transforming the validation steps to a series of ⁠expect_*()⁠ calls inside individual testthat::test_that() statements.

A major requirement for using write_testthat_file() on an agent is the presence of an expression that can retrieve the target table. Typically, we might supply a table-prep formula, which is a formula that can be invoked to obtain the target table (e.g., tbl = ~ pointblank::small_table). This user-supplied statement will be used by write_testthat_file() to generate a table-loading statement at the top of the new testthat test file so that the target table is available for each of the testthat::test_that() statements that follow. If an agent was not created using a table-prep formula set for the tbl, it can be modified via the set_tbl() function.

Thresholds will be obtained from those applied for the stop state. This can be set up for a pointblank agent by passing an action_levels object to the actions argument of create_agent() or the same argument of any included validation function. If stop thresholds are not available, then a threshold value of 1 will be used for each generated ⁠expect_*()⁠ statement in the resulting testthat test file.

There is no requirement that the agent first undergo interrogation with interrogate(). However, it may be useful as a dry run to interactively perform an interrogation on the target data before generating the testthat test file.

Usage

write_testthat_file(
  agent,
  name = NULL,
  path = NULL,
  overwrite = FALSE,
  skips = NULL,
  quiet = FALSE
)

Arguments

agent	The pointblank agent object ⁠obj:<ptblank_agent>⁠ // required A pointblank agent object that is commonly created through the use of the create_agent() function.
name	Name for generated testthat file ⁠scalar<character>⁠ // default: NULL (optional) An optional name for for the testhat test file. This should be a name without extension and without the leading "test-" text. If nothing is supplied, the name will be derived from the tbl_name in the agent. If that's not present, a generic name will be used.
path	File path ⁠scalar<character>⁠ // default: NULL (optional) A path can be specified here if there shouldn't be an attempt to place the file in testthat/tests.
overwrite	Overwrite a previous file of the same name ⁠scalar<logical>⁠ // default: FALSE Should a testthat file of the same name be overwritten?
skips	Test skipping ⁠vector<character>⁠ // default: NULL (optional) This is an optional vector of test-skipping keywords modeled after the testthat ⁠skip_on_*()⁠ functions. The following keywords can be used to include ⁠skip_on_*()⁠ statements: "cran" (testthat::skip_on_cran()), "travis" (testthat::skip_on_travis()), "appveyor" (testthat::skip_on_appveyor()), "ci" (testthat::skip_on_ci()), "covr" (testthat::skip_on_covr()), "bioc" (testthat::skip_on_bioc()). There are keywords for skipping tests on certain operating systems and all of them will insert a specific testthat::skip_on_os() call. These are "windows" (skip_on_os("windows")), "mac" (skip_on_os("mac")), "linux" (skip_on_os("linux")), and "solaris" (skip_on_os("solaris")). These calls will be placed at the top of the generated testthat test file.
quiet	Inform (or not) upon file writing ⁠scalar<logical>⁠ // default: FALSE Should the function not inform when the file is written?

Details

Tests for inactive validation steps will be skipped with a clear message indicating that the reason for skipping was due to the test not being active. Any inactive validation steps can be forced into an active state by using the activate_steps() on an agent (the opposite is possible with the deactivate_steps() function).

The testthat package comes with a series of ⁠skip_on_*()⁠ functions which conveniently cause the test file to be skipped entirely if certain conditions are met. We can quickly set any number of these at the top of the testthat test file by supplying keywords as a vector to the skips option of write_testthat_file(). For instance, setting ⁠skips = c("cran", "windows)⁠ will add the testthat skip_on_cran() and skip_on_os("windows") statements, meaning that the generated test file won't run on a CRAN system or if the system OS is Windows.

Here is an example of testthat test file output ("test-small_table.R"):

# Generated by pointblank

tbl <- small_table

test_that("column `date_time` exists", {
  
  expect_col_exists(
    tbl,
    columns = date_time,
    threshold = 1
  ) 
})

test_that("values in `c` should be <= `5`", {
  
  expect_col_vals_lte(
    tbl,
    columns = c,
    value = 5,
    threshold = 0.25
  ) 
})

This was generated by the following set of R statements:

library(pointblank)

agent <- 
  create_agent(
    tbl = ~ small_table,
    actions = action_levels(stop_at = 0.25)
  ) %>%
  col_exists(date_time) %>%
  col_vals_lte(c, value = 5)
  
write_testthat_file(
  agent = agent,
  name = "small_table",
  path = "."
)

Value

Invisibly returns TRUE if the testthat file has been written.

Examples

Creating a testthat file from an agent

Let's walk through a data quality analysis of an extremely small table. It's actually called small_table and we can find it as a dataset in this package.

small_table
#> # A tibble: 13 x 8
#>    date_time           date           a b             c      d e     f    
#>    <dttm>              <date>     <int> <chr>     <dbl>  <dbl> <lgl> <chr>
#>  1 2016-01-04 11:00:00 2016-01-04     2 1-bcd-345     3  3423. TRUE  high 
#>  2 2016-01-04 00:32:00 2016-01-04     3 5-egh-163     8 10000. TRUE  low  
#>  3 2016-01-05 13:32:00 2016-01-05     6 8-kdg-938     3  2343. TRUE  high 
#>  4 2016-01-06 17:23:00 2016-01-06     2 5-jdo-903    NA  3892. FALSE mid  
#>  5 2016-01-09 12:36:00 2016-01-09     8 3-ldm-038     7   284. TRUE  low  
#>  6 2016-01-11 06:15:00 2016-01-11     4 2-dhe-923     4  3291. TRUE  mid  
#>  7 2016-01-15 18:46:00 2016-01-15     7 1-knw-093     3   843. TRUE  high 
#>  8 2016-01-17 11:27:00 2016-01-17     4 5-boe-639     2  1036. FALSE low  
#>  9 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9   838. FALSE high 
#> 10 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9   838. FALSE high 
#> 11 2016-01-26 20:07:00 2016-01-26     4 2-dmx-010     7   834. TRUE  low  
#> 12 2016-01-28 02:51:00 2016-01-28     2 7-dmx-010     8   108. FALSE low  
#> 13 2016-01-30 11:23:00 2016-01-30     1 3-dka-303    NA  2230. TRUE  high

Creating an action_levels object is a common workflow step when creating a pointblank agent. We designate failure thresholds to the warn, stop, and notify states using action_levels().

al <- 
  action_levels(
    warn_at = 0.10,
    stop_at = 0.25,
    notify_at = 0.35
  )

A pointblank agent object is now created and the al object is provided to the agent. The static thresholds provided by the al object make reports a bit more useful after interrogation.

agent <- 
  create_agent(
    tbl = ~ small_table,
    label = "An example.",
    actions = al
  ) %>%
  col_exists(c(date, date_time)) %>%
  col_vals_regex(
    b,
    regex = "[0-9]-[a-z]{3}-[0-9]{3}"
  ) %>%
  col_vals_gt(d, value = 100) %>%
  col_vals_lte(c, value = 5) %>%
  interrogate()

This agent and all of the checks can be transformed into a testthat file with write_testthat_file(). The stop thresholds will be ported over to the ⁠expect_*()⁠ functions in the new file.

write_testthat_file(
  agent = agent,
  name = "small_table",
  path = "."
)

The above code will generate a file with the name "test-small_table.R". The path was specified with "." so the file will be placed in the working directory. If you'd like to easily add this new file to the tests/testthat directory then path = NULL (the default) will makes this possible (this is useful during package development).

What's in the new file? This:

# Generated by pointblank

tbl <- small_table

test_that("column `date` exists", {
  
  expect_col_exists(
    tbl,
    columns = date,
    threshold = 1
  ) 
})

test_that("column `date_time` exists", {
  
  expect_col_exists(
    tbl,
    columns = date_time,
    threshold = 1
  ) 
})

test_that("values in `b` should match the regular expression: 
`[0-9]-[a-z]{3}-[0-9]{3}`", {
  
  expect_col_vals_regex(
    tbl,
    columns = b,
    regex = "[0-9]-[a-z]{3}-[0-9]{3}",
    threshold = 0.25
  ) 
})

test_that("values in `d` should be > `100`", {
  
  expect_col_vals_gt(
    tbl,
    columns = d,
    value = 100,
    threshold = 0.25
  ) 
})

test_that("values in `c` should be <= `5`", {
  
  expect_col_vals_lte(
    tbl,
    columns = c,
    value = 5,
    threshold = 0.25
  ) 
})

Using an agent stored on disk as a YAML file

An agent on disk as a YAML file can be made into a testthat file. The "agent-small_table.yml" file is available in the pointblank package and the path can be obtained with system.file().

yml_file <- 
  system.file(
    "yaml", "agent-small_table.yml",
    package = "pointblank"
  )

Writing the testthat file into the working directory is much the same as before but we're reading the agent from disk this time. It's a read and write combo, really. Again, we are choosing to write the file to the working directory by using path = ".".

write_testthat_file(
  agent = yaml_read_agent(yml_file),
  name = "from_agent_yaml",
  path = "."
)

Function ID

8-5

See Also

Other Post-interrogation: all_passed(), get_agent_x_list(), get_data_extracts(), get_sundered_data()

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