Define and modify BioCro module test case files

Test cases for testing modules can be stored in files. The functions here provide ways to create and update those files.

initialize_csv helps define test cases for module testing by initializing the csv file for one module based on either a set of default input values or user-supplied ones.

add_csv_row helps define test cases for module testing by adding one test case to a module's csv file based on the user-supplied inputs and description.

update_csv_cases helps define cases for module testing by updating the expected output values for each case stored in a module's csv file.

Usage

initialize_csv(
    module_name,
    directory,
    nonstandard_inputs = list(),
    description = "automatically-generated test case",
    overwrite = FALSE
  )

  add_csv_row(module_name, directory, inputs, description)

  update_csv_cases(module_name, directory)

Arguments

module_name

A string specifying one BioCro module, formatted like library_name:local_module_name, where library_name is the name of a library that contains a module with local name local_module_name; such fully-qualified module names can be formed manually or with module_paste.

directory

The directory where module test case files are stored, e.g. file.path('tests', 'module_test_cases').

inputs

A list of module inputs, i.e., a list of named numeric elements corresponding to the module's input quantities.

description

A string describing the test case, e.g. "temp above tbase". The description should be succinct and not contain any newline characters.

nonstandard_inputs

An optional list of input quantities whose values will override the default value of 1.0; see the inputs entry above.

overwrite

A logical value indicating whether an existing file should be overwritten.

Details

Module test case files form a critical component of BioCro's regression testing system. For more details, see the help page for module_testing.

The initialize_csv function will evaluate the module for a set of input quantities and store the results as a test case csv file. Typically, both of its optional arguments can be omitted. However, some modules produce errors when all inputs are set to 1.0. In this case, it would be necessary to supply some nonstandard inputs and (possibly) an alternate case description.

The add_csv_row function will evaluate the module for a set of input quantities, define a test case from the resulting outputs and the description, and add it to the module's corresponding csv file. If no csv file exists, one will be initialized with the new case.

The update_csv_cases function will evaluate the module for all input values specified in its csv case file and update the stored values of the corresponding outputs. Any output columns not present in the file will be added automatically and filled in with the correct values. Although the output columns are optional, the description column must exist in the csv file.

If a module test fails and update_csv_cases is used to update the test, care should be taken to ensure that the new outputs are sensible. This function should not be used to blindly ensure that tests pass, since a test failure may indicate a real problem with a module.

Note that update_csv_cases can be used to batch-initialize test cases. To do this, manually create a test case csv file with the proper name that only includes columns for the inputs and the description; now, calling update_csv_cases will automatically fill in the outputs for each case. With this method, care must be taken when manually specifying the values of the description column; the descriptions must be double quoted, and if they contain internal double quotes, those quotes must be doubled. Generally it is safest to simply avoid double quotes in the descriptions. (See qmethod in the help file for write.csv for more details about quoting.)

Value

A message indicating whether a file was created, overwritten, or not written.

See also

• modules

• module_paste

• module_testing

• test_module_library

• test_module

Examples

# First, we will initialize a test case file for the 'BioCro' library's
# 'thermal_time_linear' module, which will be saved in a temporary directory as
# 'BioCro_thermal_time_linear.csv'. Then, we will add a new case to the file.
# Finally, we will update the file. Note that the call to `update_csv_cases`
# will not actually modify the file unless it is manually edited beforehand to
# change an input or output value.

td <- tempdir()

initialize_csv(
  'BioCro:thermal_time_linear',
  td,
  nonstandard_inputs = list(temp = -1),
  overwrite = TRUE
)
#> [1] "Case file `/tmp/Rtmpa12Fsi/BioCro_thermal_time_linear.csv` was initialized; any pre-existing file was overwritten"

writeLines(readLines(file.path(td, 'BioCro_thermal_time_linear.csv')))
#> input,input,input,input,output,"description"
#> sowing_time,tbase,temp,time,TTc,NA
#> 1,1,-1,1,0,"automatically-generated test case"

add_csv_row(
  'BioCro:thermal_time_linear',
  td,
  list(time = 101, sowing_time = 100, tbase = 20, temp = 44),
  'temp above tbase'
)
#> [1] "Added new case to file `/tmp/Rtmpa12Fsi/BioCro_thermal_time_linear.csv`"

writeLines(readLines(file.path(td, 'BioCro_thermal_time_linear.csv')))
#> input,input,input,input,output,"description"
#> sowing_time,tbase,temp,time,TTc,NA
#> 1,1,-1,1,0,"automatically-generated test case"
#> 100,20,44,101,1,"temp above tbase"

update_csv_cases('BioCro:thermal_time_linear', td)
#> [1] "Updated case file `/tmp/Rtmpa12Fsi/BioCro_thermal_time_linear.csv`"