[Review view] SDTM Phase 3: Shiny app integration

[Gero1999]

⚠️ Review-only PR — do not merge

This is a review view into the SDTM changes from #1318. It isolates the Shiny app integration for focused code review. The actual merge will happen via #1318.

Depends on Phase 1 (#1328) and Phase 2 (#1329).

Scope

Upload step (data_upload.R)

• ADNCA/SDTM radio toggle
• SDTM mode: 3 file inputs — PC (required), EX (required), subject-level (optional, multi-file merged by STUDYID+USUBJID)
• Default SDTM example data (pc_example, ex_example, dm_example) loaded when no files uploaded
• Settings restore switches the radio toggle
• Extracted helpers: .read_sdtm_domain(), .read_subject_level_files(), .build_sdtm_result()

Mapping step (data_mapping.R)

• SDTM-specific mapping panel with 4 sections: SDTM General, PC Concentrations, EX Dosing, Supplemental Variables
• All SDTM input IDs prefixed with sdtm_ to avoid collisions with 6 shared ADNCA variable names
• Panel visibility via shinyjs::hidden()/toggle() (not conditionalPanel)
• SDTM processing: renames columns → calls sdtm_to_PKNCAdata() → stores PKNCAdata → returns conc data for filtering
• Extracted helpers: .populate_adnca_inputs(), .populate_sdtm_inputs(), .get_adnca_metabolite_selection()

NCA pipeline (tab_data.R)

• pknca_data reactive branches on mode: SDTM retrieves PKNCAdata from mapping step; ADNCA uses existing pipeline

Export (zip-utils.R)

• SDTM mode exports PC/EX/DM as separate RDS files
• Uses script_template_sdtm.R with column mapping applied from session settings

Settings (nca_setup.R, get_session_code.R)

• Settings YAML includes input_mode and sdtm_metabolites
• get_settings_code() auto-selects template based on input_mode

Files changed

File	Change
inst/shiny/modules/tab_data/data_upload.R	+309 lines — SDTM upload path, helpers
inst/shiny/modules/tab_data/data_mapping.R	+478 lines — SDTM mapping panel, helpers
inst/shiny/modules/tab_data.R	+36 lines — orchestration
inst/shiny/functions/zip-utils.R	+31 lines — SDTM export
inst/www/templates/script_template_sdtm.R	+120 lines — new template
R/get_session_code.R	+16 lines — template selection
inst/shiny/modules/tab_nca/nca_setup.R	+6 lines — settings payload
.lintr	template exclusion

What to review

• Upload flow: file validation, error handling, settings restore
• Mapping panel: input ID collision avoidance (sdtm_ prefix), column rename logic
• Data flow: sdtm_raw → mapping → sdtm_to_PKNCAdata() → filtering → NCA
• Export: separate RDS files, script template with mapping
• Edge cases: missing DM, partial uploads, metabolite selection