Feature Request: code generation feature

[rammprasad]

Feature Idea

The specification format for OAK is almost ready. Can we try the code generation feature?

The feature will accept the spec in a csv format and domain name as parameters and it will generate the R code required. We may have to make some changes to the spec as we develop this feature. It may be beneficial to add the associated topic variable for each qualifier. We can brainstorm these requirements.

Also, we can think about a JSON format as input for the specification.

Relevant Input

CM domain:
Spec - https://github.com/pharmaverse/rinpharma-2024-SDTM-workshop/blob/main/specs/cm_cdash/cm_sdtm_oak_spec_cdash.csv

VS DOmain -
Spec - https://github.com/pharmaverse/rinpharma-2024-SDTM-workshop/blob/main/specs/vs/vs_sdtm_oak_spec.csv

Relevant Output

CM domain Program - https://github.com/pharmaverse/rinpharma-2024-SDTM-workshop/blob/main/exercises/create_cm_cdash.R

VS Domain Program - Program - https://github.com/pharmaverse/rinpharma-2024-SDTM-workshop/blob/main/exercises/create_vs.R

Reproducible Example/Pseudo Code

sdtm.oak::generate_code(spec = "cm_cdash/cm_sdtm_oak_spec_cdash.csv" domain = 'cm')

[edgar-manukyan]

Thanks Ram, I will give it a try.

[edgar-manukyan]

The POC for one topic CM code generation (full domain 💯 ) is ready for discussion at #108
Please consider slightly modified specs:
cm_sdtm_oak_spec_cdash.csv

The code to run:

• download the specs into project dir
• run the following:

spec <- read_spec("cm_sdtm_oak_spec_cdash.csv")

spec <- spec |>
  dplyr::filter(
    !is.na(target_sdtm_variable),
    !is.na(mapping_algorithm),
    !target_sdtm_variable %in% c("DOMAIN")
  )

domain <- "cm"
generate_code(spec, domain)

• If you want a nicer code, though a bit longer then change width:

# One can use option width to control the width of the code
# Twenty will almost always place every parameter on a separate line
old_width <- options(width = 20)
generate_code(spec, domain)
# Restore original width
options(width = old_width$width)

Generated code

• changed extension to txt for upload, please change to R
  cm_sdtm_oak_code.txt

Generated cm

• cm.csv

[edgar-manukyan]

Multi-topic VS poc

Spec

• vs_sdtm_oak_spec.csv

Generated code

• vs_sdtm_oak_code.txt, please change the extension to .R

Resultant vs

• vs.csv

Also, please consider the updated cm spec

• cm_sdtm_oak_spec_cdash.csv