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@lauramaxwell lauramaxwell released this 15 May 13:41
v1.1.4
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gsm.mapping v1.1.4

This patch release updates the GitHub action workflows to align with the new federated action framework in gsm.utils

What's Changed

Full Changelog: v1.1.3...v1.1.4

{qcthat} Reports

Completed Issues

✅ A qcthat issue test matrix with 3 milestones, 29 issues, and 11 tests 
├─█─Milestone: v1.1.0 (4 issues, 0 tests)
│ ├─☑️─Requirement 62: Business Requirement:  Add AE domains to data model
│ │ └─(no tests)
│ ├─☑️─Issue 61: Request New Domain or Variable: Dates
│ │ └─(no tests)
│ ├─☑️─Issue 35: Feature: Additional AE fields
│ │ └─(no tests)
│ └─☑️─Issue 34: Feature: Add "category" to PD.yaml
│   └─(no tests)
├─█─Milestone: v1.1.2 (2 issues, 0 tests)
│ ├─☑️─Feature 104: Make modifications to `EXCLUSION.yaml` to tweak text of ineligibility related components for legibility
│ │ └─(no tests)
│ └─☑️─Technical Task 91: Add `db_lock_dt` to `STUDY` domain
│   └─(no tests)
├─█─Milestone: v1.1.3 (4 issues, 3 tests)
│ ├─☑️─Technical Task 114: Add a new `death_days` column to `DEATH` domain
│ │ ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│ │ └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│ ├─☑️─Bug 112: Remove `setdiff` call for `db_lock_dt`
│ │ └─(no tests)
│ ├─☑️─Bug 101: Fix data types in AE, PK and SUBJ
│ │ └─(no tests)
│ └─☑️─Technical Task 97: Migrate appropriate qualification tests to gsm.mapping
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│   └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 3 mappings are completed as expected (#97)
└─█─Milestone: <none> (19 issues, 8 tests)
  ├─☑️─Issue 72: Feature: Include study ID in all data specifications.
  │ └─(no tests)
  ├─☑️─Issue 29: Feature: Create Issue templates for adding and editing new domain
  │ └─(no tests)
  ├─☑️─Issue 28: Feature: Add  `{gsm.endpoints}` mapping workflows
  │ └─(no tests)
  ├─☑️─Issue 25: Updates to Mapping Specification VIgnette
  │ └─(no tests)
  ├─☑️─Issue 24: Remove `util-` from file names
  │ └─(no tests)
  ├─☑️─Issue 21: refactor yamls to remove `_all` param/field
  │ └─(no tests)
  ├─☑️─Issue 20: Move additional data wrangling functions from gsm
  │ └─(no tests)
  ├─☑️─Issue 6: Feature: Expand AE.yaml
  │ └─(no tests)
  ├─☑️─Issue 5: Feature: Expand SUBJ.yaml
  │ └─(no tests)
  ├─☑️─Issue 2: Add ingestion-related functions
  │ ├─✅─Combining multiple specs with overlapping dfs, deduplicating cols (#2)
  │ ├─✅─Combining specs with non-overlapping dfs (#2)
  │ ├─✅─Combining specs with some empty dfs (#2)
  │ ├─✅─Combining empty list of specs returns an empty list (#2)
  │ ├─✅─Combining a single spec returns the same spec (#2)
  │ ├─✅─Combining specs with NULL entries is handled correctly (#2)
  │ ├─✅─warning if type doesn't match first instance (#2)
  │ └─✅─Ingest works with optional columns (#2)
  ├─☑️─Issue 1: Add mapping yamls from `{gsm}` 
  │ └─(no tests)
  ├─☑️─Bug 70: Data specification of `_all` coerces all columns to character.
  │ └─(no tests)
  ├─☑️─Technical Task 58: Request New Domain or Variable:  IE domain
  │ └─(no tests)
  ├─☑️─Issue 55: Keep Specified Columns
  │ └─(no tests)
  ├─☑️─Issue 53: Feature: Merge visit schedule onto PK domain.
  │ └─(no tests)
  ├─☑️─Issue 50: Bugfix: Fix source column names for endpoints mappings
  │ └─(no tests)
  ├─☑️─Issue 38: Add PK yaml
  │ └─(no tests)
  ├─☑️─Issue 37: Feature: Swap clindata with gsm.datasim
  │ └─(no tests)
  └─☑️─Issue 30: QC: Namespace all functions in workflow yamls
    └─(no tests)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

⭕ 26 issues lack tests

🙈 12 issues with label "qcthat-nocov" were ignored

This report was run locally by Laura Maxwell (@lauramaxwell) due to a bug in the qcthat package (Documented here)

Session Info ─ Session info ───────────────────────────────────────────────────────────────────────────

! setting value
version R version 4.5.1 (2025-06-13 ucrt)
os Windows 11 x64 (build 26200)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Europe.utf8
ctype English_Europe.utf8
tz America/New_York
date 2026-05-18
rstudio 2025.09.2+418 Cucumberleaf Sunflower (desktop)
pandoc 3.9 @ C:\Users\Laura Maxwell\AppData\Local\Pandoc/ (via rmarkdown)
quarto @ C:\PROGRA1\RStudio\RESOUR1\app\bin\quarto\bin\quarto.exe

─ Packages ────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
askpass 1.2.1 2024-10-04 [1] CRAN (R 4.5.1)
brio 1.1.5 2024-04-24 [1] CRAN (R 4.4.0)
cli 3.6.6 2026-04-09 [1] CRAN (R 4.4.3)
credentials 2.0.3 2025-09-12 [1] CRAN (R 4.4.3)
curl 7.0.0 2025-08-19 [1] CRAN (R 4.4.3)
DBI 1.3.0 2026-02-25 [1] CRAN (R 4.4.3)
dbplyr 2.5.2 2026-02-13 [1] CRAN (R 4.4.3)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.5.1)
dplyr 1.2.1 2026-04-03 [1] CRAN (R 4.4.3)
duckdb 1.5.2 2026-04-13 [1] CRAN (R 4.4.3)
evaluate 1.0.5 2025-08-27 [1] CRAN (R 4.5.1)
generics 0.1.4 2025-05-09 [1] CRAN (R 4.5.1)
gert 2.3.1 2026-01-11 [1] CRAN (R 4.4.3)
gh 1.5.0 2025-05-26 [1] CRAN (R 4.5.1)
gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.5.1)
glue 1.8.1 2026-04-17 [1] CRAN (R 4.4.1)
gsm.core 1.2.0 2026-04-17 [1] Github (Gilead-BioStats/gsm.core@43cfd09)
gsm.mapping * 1.1.4 2026-04-17 [?] Github (f26203b)
httr2 1.2.2 2025-12-08 [1] CRAN (R 4.4.3)
jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.4.3)
lifecycle 1.0.5 2026-01-08 [1] CRAN (R 4.4.3)
log4r 0.4.4 2024-10-12 [1] CRAN (R 4.4.2)
magrittr 2.0.5 2026-04-04 [1] CRAN (R 4.4.3)
openssl 2.3.4 2025-09-30 [1] CRAN (R 4.4.3)
otel 0.2.0 2025-08-29 [1] CRAN (R 4.4.3)
pillar 1.11.1 2025-09-17 [1] CRAN (R 4.4.3)
pkgbuild 1.4.8 2025-05-26 [1] CRAN (R 4.5.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.5.1)
pkgload 1.5.1 2026-04-01 [1] CRAN (R 4.4.3)
purrr 1.2.2 2026-04-10 [1] CRAN (R 4.4.3)
qcthat 1.1.0.9000 2026-02-26 [1] Github (Gilead-Public/qcthat@93eefd0)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.5.1)
rappdirs 0.3.4 2026-01-17 [1] CRAN (R 4.4.3)
rlang 1.2.0 2026-04-06 [1] CRAN (R 4.4.3)
rprojroot 2.1.1 2025-08-26 [1] CRAN (R 4.5.1)
rstudioapi 0.18.0 2026-01-16 [1] CRAN (R 4.4.3)
sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.5.1)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.4.3)
stringr 1.6.0 2025-11-04 [1] CRAN (R 4.4.3)
sys 3.4.3 2024-10-04 [1] CRAN (R 4.4.1)
testthat * 3.3.2 2026-01-11 [1] CRAN (R 4.4.3)
tibble 3.3.1 2026-01-11 [1] CRAN (R 4.4.3)
tidyr 1.3.2 2025-12-19 [1] CRAN (R 4.4.3)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.1)
vctrs 0.7.3 2026-04-11 [1] CRAN (R 4.4.3)
waldo 0.6.2 2025-07-11 [1] CRAN (R 4.5.1)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.5.1)
yaml * 2.3.12 2025-12-10 [1] CRAN (R 4.4.3)

Contributors

lauramaxwell and jonthegeek
Assets 4
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