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pharmaverse / sdtm.oak

An EDC and Data Standard agnostic SDTM data transformation engine that automates the transformation of raw clinical data in ODM format to SDTM based on standard mapping algorithms
https://pharmaverse.github.io/sdtm.oak/
Apache License 2.0
30 stars 13 forks source link

Feature Request: code generation feature #107

Open rammprasad opened 2 days ago

rammprasad commented 2 days ago

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 commented 2 days ago

Thanks Ram, I will give it a try.