feat: add log-points for NCA user input changes by Gero1999 · Pull Request #1221 · pharmaverse/aNCA

Gero1999 · 2026-04-14T12:56:37Z

Issue

Description

Adds INFO-level logging for user input changes across the NCA setup modules so that exported session_log.txt files capture what configuration choices the user made — not just that a calculation happened.

New log-points added:

Settings — analyte, specimen, profile, extrapolation method, min half-life points, flag rule enable/disable and threshold changes
Data Imputation — BLQ strategy changes, C0 imputation toggle
Parameter Selection — full parameter list at DEBUG level (count was already logged at INFO)
Slope Selector — rule add/remove upgraded from TRACE→INFO, DEBUG summary of rule counts on table change
General Exclusions — exclusion add (with row count, type, reason), removal, settings restore

Definition of Done

Log messages appear in the R console when users change NCA settings, parameters, slope rules, or exclusions
Messages are included in the ZIP-exported session_log.txt
No logging on reactive invalidation noise — only meaningful user actions

How to test

Run aNCA::run_app()
Upload data and navigate to the NCA tab
Change settings (method, analyte, specimen, flag rules, etc.)
Add/remove slope rules and exclusions
Verify log messages appear in the R console for each action
Export ZIP and check session_log.txt contains the entries

Contributor checklist

Code passes lintr checks
Code passes all unit tests
New logic covered by unit tests
New logic is documented
App or package changes are reflected in NEWS
Package version is incremented
R script works with the new implementation (if applicable)
Settings upload works with the new implementation (if applicable)
If any .scss change was done, run data-raw/compile_css.R

Notes to reviewer

This PR targets 1210-enhancement/replace-logger-with-console (#1212), not main. It will auto-retarget to main once #1212 is merged.

All log calls use the same log_info/log_debug functions introduced in #1212 — no new dependencies.

Version bump and NEWS entry still needed before merge.

Log analyte, specimen, profile, method, min half-life points, and flag rule changes at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log the full list of selected parameters at DEBUG level alongside the existing INFO count message. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Upgrade slope rule add/remove from TRACE to INFO level. Add DEBUG summary of slope rules count on table changes. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log exclusion add (with row count, type, reason), removal, and settings restore at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log NCA profile changes, BLQ strategy changes, and C0 imputation toggle at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Replace all glue-style log calls ({var}) with paste-style (multiple arguments) to avoid parent.frame(2) scoping issues in closures and observeEvent callbacks. Guard profile log against NA values. Co-authored-by: Ona <no-reply@ona.com>

Log analyte, specimen, profile, method, min half-life points, and flag rule changes at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log the full list of selected parameters at DEBUG level alongside the existing INFO count message. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Upgrade slope rule add/remove from TRACE to INFO level. Add DEBUG summary of slope rules count on table changes. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log exclusion add (with row count, type, reason), removal, and settings restore at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Log NCA profile changes, BLQ strategy changes, and C0 imputation toggle at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Replace all glue-style log calls ({var}) with paste-style (multiple arguments) to avoid parent.frame(2) scoping issues in closures and observeEvent callbacks. Guard profile log against NA values. Co-authored-by: Ona <no-reply@ona.com>

…b.com/pharmaverse/aNCA into 1219-enhancement/nca-input-log-points

Copilot

Pull request overview

This PR adds INFO/DEBUG logging across the Shiny NCA setup modules so exported session_log.txt captures user configuration changes (settings, imputation, parameter selection, slope rules, exclusions), improving post-hoc traceability of an NCA run.

Changes:

Added log points for selection changes (analyte/specimen/profile, extrapolation method, min half-life points, flag rules).
Added log points for BLQ and C0 imputation setting changes.
Added more detailed logging for slope rule and exclusion add/remove/restore actions, plus DEBUG summaries.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
inst/shiny/modules/tab_nca/setup/slope_selector.R	Adds DEBUG summary log when manual slope rules table updates.
inst/shiny/modules/tab_nca/setup/settings.R	Adds INFO logs for key NCA settings and flag-rule changes.
inst/shiny/modules/tab_nca/setup/parameter_selection.R	Adds DEBUG log listing selected parameters per study type.
inst/shiny/modules/tab_nca/setup/manual_slopes_table.R	Upgrades add/remove slope rule logs from TRACE to INFO.
inst/shiny/modules/tab_nca/setup/general_exclusions.R	Adds INFO logs for exclusions restored/added/removed.
inst/shiny/modules/tab_nca/setup/data_imputation.R	Adds INFO logs for BLQ strategy and C0 imputation toggle changes.

+      if (length(target_profile) > 0 && !anyNA(target_profile)) {
+        log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
+      }


      if (updating_filters()) return()
      updating_filters(TRUE)
      on.exit(updating_filters(FALSE))

+      log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))


      if (updating_filters()) return()
      updating_filters(TRUE)
      on.exit(updating_filters(FALSE))

+      log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))


+      rows_sel <- getReactableState("conc_table-table", "selected")
+      reason <- input$exclusion_reason
+      nca_checked <- isTRUE(input$cb_manual_nca)
+      tlg_checked <- isTRUE(input$cb_tlg)
+
+      if (length(rows_sel) > 0 && nzchar(reason) && (nca_checked || tlg_checked)) {
+        type_label <- if (nca_checked && tlg_checked) "NCA + TLG"
+          else if (nca_checked) "NCA"
+          else "TLG"
+        log_info(
+          "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+          ", reason='", reason, "'"
+        )
+      }
+
      .handle_add_exclusion(
        input, session, exclusion_list, xbtn_counter
      )


    # Add a new row to the table when the user clicks the add button
    observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_info("Slope selector: adding manual slope rule")


    # Remove selected rows from the table when the user clicks the remove button
    observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_info("Slope selector: removing manual slope rule")


+      n_rules <- nrow(manual_slopes())
+      n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+      n_incl <- n_rules - n_excl
+      log_debug("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")


Gero1999 and others added 5 commits April 14, 2026 10:03

feat: add log-points for NCA settings changes

41b9403

Log analyte, specimen, profile, method, min half-life points, and flag rule changes at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add debug log-point for selected parameter names

5922af8

Log the full list of selected parameters at DEBUG level alongside the existing INFO count message. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for slope selector user actions

7ce0384

Upgrade slope rule add/remove from TRACE to INFO level. Add DEBUG summary of slope rules count on table changes. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for general exclusion changes

ef5b7de

Log exclusion add (with row count, type, reason), removal, and settings restore at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for profile selection and data imputation

4a4b92d

Log NCA profile changes, BLQ strategy changes, and C0 imputation toggle at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Gero1999 mentioned this pull request Apr 14, 2026

docs: document session log contents #1222

Merged

9 tasks

Gero1999 requested review from Shaakon35, bachapman and js3110 April 14, 2026 12:59

Gero1999 marked this pull request as ready for review April 14, 2026 13:00

Gero1999 removed request for Shaakon35, bachapman and js3110 April 14, 2026 13:01

Gero1999 marked this pull request as draft April 14, 2026 13:01

Gero1999 and others added 7 commits April 14, 2026 13:20

feat: add log-points for NCA settings changes

47f533b

Log analyte, specimen, profile, method, min half-life points, and flag rule changes at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add debug log-point for selected parameter names

550e0bb

Log the full list of selected parameters at DEBUG level alongside the existing INFO count message. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for slope selector user actions

b378504

Upgrade slope rule add/remove from TRACE to INFO level. Add DEBUG summary of slope rules count on table changes. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for general exclusion changes

1227387

Log exclusion add (with row count, type, reason), removal, and settings restore at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

feat: add log-points for profile selection and data imputation

dacc0c2

Log NCA profile changes, BLQ strategy changes, and C0 imputation toggle at INFO level. Closes #1219 (partial) Co-authored-by: Ona <no-reply@ona.com>

Gero1999 force-pushed the 1219-enhancement/nca-input-log-points branch from 91ca90b to 893084b Compare April 14, 2026 15:34

Merge branch '1219-enhancement/nca-input-log-points' of https://githu…

2f0b9d8

…b.com/pharmaverse/aNCA into 1219-enhancement/nca-input-log-points

Gero1999 requested a review from Copilot April 16, 2026 07:04

Copilot started reviewing on behalf of Gero1999 April 16, 2026 07:04 View session

Copilot AI reviewed Apr 16, 2026

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feat: add log-points for NCA user input changes#1221

feat: add log-points for NCA user input changes#1221
Gero1999 wants to merge 13 commits into1210-enhancement/replace-logger-with-consolefrom
1219-enhancement/nca-input-log-points

Gero1999 commented Apr 14, 2026 •

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Gero1999 commented Apr 14, 2026 •

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