whirl

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Overview

The whirl package provide functionalities for executing scripts in batch and simultaneously getting a log from the individual executions. A log from script execution is in many pharmaceutical companies a GxP requirement, and the whirl package honors this requirement by generating a log that, among other things, contains information about:

And all this is wrapped into a nicely formatted html document that is easy to navigate.

Installation

# Install the released version from CRAN:
install.packages("whirl")
# Install the development version from GitHub:
pak::pak("NovoNordisk-OpenSource/whirl")

Usage

The main function in the whirl package is run() which takes an input argument that defines the scripts to be executed.

The simplest way is to provide the path to a single script:

library(whirl)

run("success.R")
#> ✔ success.R: Completed succesfully

It is also possible to run several scripts simultaneously:

result <- run(c("success.R", "warning.R"), n_workers = 2)
#> ✔ success.R: Completed succesfully
#> ⚠ warning.R: Completed with warnings

Here we are specifying that run() can use up to two simultaneous workers to execute the scripts, meaning that they will be executed in parallel.

When using run() the following files are created:

  1. Creates a log in the same directory as the script with the names {script_name}_log.html. See example_log.html for an example of a simple log.
  2. Creates a summary log with the overall status of each script. Default path is summary.html. See summary.html for an example of a summary of the same log as above.

Apart from this the function also returns a tibble with the status of the script execution similar to the content of the summary above:

print(result)
#> # A tibble: 2 × 6
#>      id tag   script                                 status result       log_dir
#>   <dbl> <chr> <chr>                                  <chr>  <list>       <chr>  
#> 1     1 <NA>  /private/var/folders/fx/71by3f551qzb5… succe… <named list> /priva…
#> 2     2 <NA>  /private/var/folders/fx/71by3f551qzb5… warni… <named list> /priva…

Config files

run() also supports running scripts in several sequential steps. This setup is very useful when your projects have several steps that depends on each others output, and thereby need to be executed in a specific order. The best way to implement this in your project is use a configuration file for whirl. The configuration file is a yaml file that specifies each steps:

_whirl.yaml:

steps:
  - name: "First step"
    paths:
      - "success.R"
  - name: "Second step"
    paths:
      - "warning.R"
      - "error.R"``

Here we are specifying that in the first step we run succes.R. And then when this step has been completed we continue to running the scripts in the second steps.

result <- run("_whirl.yaml", n_workers = 2)
#> ✔ success.R: Completed succesfully
#> ⚠ warning.R: Completed with warnings
#> ✖ error.R: Completed with errors
print(result)
#> # A tibble: 3 × 6
#>      id tag   script                                 status result       log_dir
#>   <dbl> <chr> <chr>                                  <chr>  <list>       <chr>  
#> 1     1 <NA>  /private/var/folders/fx/71by3f551qzb5… succe… <named list> /priva…
#> 2     2 <NA>  /private/var/folders/fx/71by3f551qzb5… warni… <named list> /priva…
#> 3     3 <NA>  /private/var/folders/fx/71by3f551qzb5… error  <named list> /priva…

For more information about how to customize the the execution and the logging for your needs see the following: