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Closes #43 test: add gh-mocked coverage for snapshot helpers#48

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Zelos Zhu (zdz2101) wants to merge 4 commits into
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fix-43
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Closes #43 test: add gh-mocked coverage for snapshot helpers#48
Zelos Zhu (zdz2101) wants to merge 4 commits into
devfrom
fix-43

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@zdz2101 Zelos Zhu (zdz2101) commented May 14, 2026

Overview

  • adds a mockable gh_api() seam and routes snapshot helper gh calls through it in:
    • R/utils-github.R
    • R/utils-workflows.R
  • adds first-pass testthat coverage for snapshot helpers with mocked gh responses in:
    • tests/testthat/test-snapshot-gh-mocks.R
  • covers key paths for:
    • resolve_package() explicit ref resolution
    • resolve_package() date-based fallback resolution
    • malformed gh commit lookup handling
    • gh_list_contents() parsing behavior
    • pull_workflows() skip and dispatch behavior

Test Notes/Sample Code

  • local install and targeted tests:
    • pak::local_install('.', dependencies = FALSE, upgrade = FALSE, ask = FALSE)
    • testthat::test_file('tests/testthat/test-manifest-terminology.R')
    • testthat::test_file('tests/testthat/test-snapshot-gh-mocks.R')

Connected Issues

@zdz2101
test: add gh-mocked coverage for snapshot helpers
9c07c3c 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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{qcthat} Report: User Acceptance

No issues are awaiting UAT.

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 18:03:07 UTC

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

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[1] /home/runner/work/_temp/Library

[2] /opt/R/4.6.0/lib/R/site-library

[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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{qcthat} Reports

PR-Associated Issues

█ A qcthat issue test matrix with 1 milestone, 1 issue, and 0 tests 
└─█─Milestone: v1.1.0 (1 issue, 0 tests)
  └─📥─Issue 43: [workr] Add testthat coverage for pull_workflows and resolve_package
    └─(no tests)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
⭕ 1 issue lacks tests

Completed Issues

🚫 A qcthat issue test matrix with 1 milestone, 5 issues, and 78 tests 
├─█─Milestone: v1.0.0 (3 issues, 71 tests)
│ ├─☑️─Issue 26: Improve unit test coverage for v1.0 release
│ │ ├─✅─MakeWorkflowList loads YAML and RunStep executes workflow correctly #26
│ │ ├─✅─Complex workflow: multi-step loaded from YAML and executed end-to-end #26
│ │ ├─✅─Workflow from YAML loads and executes with meta reference #26
│ │ ├─✅─loadExample returns input data when initData.R is missing (#9, #26)
│ │ ├─✅─loadExample loads initData.R and merges with lData (#9, #26)
│ │ ├─✅─loadExample validates initData return type (#9, #26)
│ │ ├─✅─loadExample does not create duplicate names on repeated calls (#9, #26)
│ │ ├─✅─MakeWorkflowList output is a named list with expected structure #26
│ │ ├─✅─MakeWorkflowList returns metadata as expected #26
│ │ ├─✅─MakeWorkflowList errors on invalid strPath #26
│ │ ├─✅─MakeWorkflowList errors on invalid strPackage #26
│ │ ├─✅─MakeWorkflowList filters by strNames #26
│ │ ├─✅─MakeWorkflowList bExact filters exactly #26
│ │ ├─✅─MakeWorkflowList names list elements by meta$ID #26
│ │ ├─✅─MakeWorkflowList sorts by Priority #26
│ │ ├─✅─MakeWorkflowList sets default Priority to 0 #26
│ │ ├─✅─MakeWorkflowList loads from package #26
│ │ ├─✅─MakeWorkflowList bRecursive finds nested workflows #26
│ │ ├─✅─RunProject runs all phases in sorted order #26
│ │ ├─✅─RunProject passes data between phases #26
│ │ ├─✅─RunProject respects strPhases subset and order #26
│ │ ├─✅─RunProject errors on missing strPath #26
│ │ ├─✅─RunProject errors on missing requested phases #26
│ │ ├─✅─RunProject errors on empty project directory #26
│ │ ├─✅─RunProject bReturnResult and bKeepInputData pass through #26
│ │ ├─✅─RunQuery returns correct result (#26)
│ │ ├─✅─RunQuery handles empty df #26
│ │ ├─✅─RunQuery handles invalid input #26
│ │ ├─✅─RunQuery checks if strQuery contains 'FROM df' #26
│ │ ├─✅─RunQuery applies schema appropriately #26
│ │ ├─✅─RunQuery applies incomplete schema appropriately #26
│ │ ├─✅─RunQuery parses invalid date/times correctly #26
│ │ ├─✅─RunQuery requires lColumnMapping when bUseSchema is TRUE #26
│ │ ├─✅─RunStep handles lMeta and lData parameters correctly #26
│ │ ├─✅─RunStep handles parameters referencing elements within lMeta and lData #26
│ │ ├─✅─RunStep passes direct value parameters correctly #26
│ │ ├─✅─RunStep passes direct value vector parameters correctly #26
│ │ ├─✅─RunStep handles multiple parameters and function invocation correctly #26
│ │ ├─✅─RunStep will run a function from a namespace #26
│ │ ├─✅─RunStep will run a function without a namespace #26
│ │ ├─✅─RunStep will run a function with no parameters #26
│ │ ├─✅─RunStep recognizes rlang::expr() string parameters #26
│ │ ├─✅─RunStep recognizes expr() shorthand parameters #26
│ │ ├─✅─RunStep recognizes rlang::exprs() parameters #26
│ │ ├─✅─RunStep recognizes exprs() shorthand parameters #26
│ │ ├─✅─RunStep passes lSpec parameter correctly #26
│ │ ├─✅─RunWorkflow returns final step result by default #26
│ │ ├─✅─RunWorkflow returns full workflow object when bReturnResult = FALSE #26
│ │ ├─✅─RunWorkflow bKeepInputData = FALSE removes input data from lData #26
│ │ ├─✅─RunWorkflow bKeepInputData = TRUE preserves input data in lData #26
│ │ ├─✅─RunWorkflow multi-step preserves intermediate results in lData #26
│ │ ├─✅─RunWorkflow invokes lConfig$LoadData #26
│ │ ├─✅─RunWorkflow invokes lConfig$SaveData on bReturnResult = TRUE #26
│ │ ├─✅─RunWorkflow validates spec when present #26
│ │ ├─✅─RunWorkflow runs without spec #26
│ │ ├─✅─RunWorkflow runs with YAML files #26
│ │ ├─✅─RunWorkflows returns named list #26
│ │ ├─✅─RunWorkflows passes prior workflow results as data to later workflows #26
│ │ ├─✅─RunWorkflows custom strResultNames #26
│ │ ├─✅─RunWorkflows passes lConfig through to RunWorkflow #26
│ │ └─✅─RunWorkflows handles empty workflow list #26
│ ├─☑️─Issue 25: Differentiate package manifests from execution snapshots
│ │ ├─✅─pkgManifest function exists #25
│ │ ├─✅─pkgManifest has correct parameters #25
│ │ ├─✅─pkgSnapshot function name is deprecated/removed #25
│ │ └─✅─pkgListFromManifest references correct function #25
│ └─☑️─Issue 19: Remove Legacy /site Explorer From workr
│   ├─✅─site/ directory does not exist #19
│   ├─✅─site-build.yaml workflow does not exist #19
│   ├─✅─site-deploy.yaml workflow does not exist #19
│   ├─✅─pkgdown-all.yaml has no Node/explorer steps #19
│   ├─✅─_pkgdown.yml has no explorer navbar entry #19
│   └─✅─.gitignore has no site/node_modules/ entry #19
└─█─Milestone: <none> (2 issues, 11 tests)
  ├─☑️─Issue 34: Finalize inst/workflows and demo Shiny app for shinyapps.io deployment
  │ ├─✅─03_AEKRI directory does not exist #34
  │ ├─✅─03_KRI initData.R does not reference gsm.core::lSource #34
  │ ├─✅─03_KRI initData.R does not reference PD domain #34
  │ ├─✅─03_KRI initData.R uses clindata package #34
  │ ├─✅─03_KRI initData.R returns Raw_SUBJ and Raw_AE #34
  │ ├─🚫─03_KRI RunWorkflows completes without error using initData #34
  │ └─✅─README contains link to hosted shinyapps.io demo #34
  └─☑️─Feature 9: Create Test data to initialize workflows
    ├─✅─loadExample returns input data when initData.R is missing (#9, #26)
    ├─✅─loadExample loads initData.R and merges with lData (#9, #26)
    ├─✅─loadExample validates initData return type (#9, #26)
    └─✅─loadExample does not create duplicate names on repeated calls (#9, #26)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
🚫 1 test was skipped

🟢 All issues have at least one test

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

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 18:03:09 UTC

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

setting value

version R version 4.6.0 (2026-04-24)

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date 2026-05-15

pandoc 3.1.3 @ /usr/bin/pandoc

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─ Packages ───────────────────────────────────────────────────────────────────

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digest 0.6.39 2025-11-19 [1] RSPM

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duckdb 1.5.2 2026-04-13 [1] RSPM

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evaluate 1.0.5 2025-08-27 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

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generics 0.1.4 2025-05-09 [1] RSPM

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gh 1.5.0 2025-05-26 [1] RSPM

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gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.1 2026-04-17 [1] RSPM

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grDevices * 4.6.0 2026-04-24 [3] local

grid 4.6.0 2026-04-24 [3] local

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jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [3] CRAN (R 4.6.0)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [3] CRAN (R 4.6.0)

lifecycle 1.0.5 2026-01-08 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [3] CRAN (R 4.6.0)

Matrix 1.7-5 2026-03-21 [3] CRAN (R 4.6.0)

memoise 2.0.1 2021-11-26 [1] RSPM

methods * 4.6.0 2026-04-24 [3] local

mgcv 1.9-4 2025-11-07 [3] CRAN (R 4.6.0)

mime 0.13 2025-03-17 [1] RSPM

nlme 3.1-169 2026-03-27 [3] CRAN (R 4.6.0)

nnet 7.3-20 2025-01-01 [3] CRAN (R 4.6.0)

openssl 2.4.1 2026-05-14 [1] RSPM

otel 0.2.0 2025-08-29 [1] RSPM

pak 0.9.5 2026-04-27 [2] local

parallel 4.6.0 2026-04-24 [3] local

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgload 1.5.2 2026-04-22 [1] RSPM

praise 1.0.0 2015-08-11 [1] RSPM

processx 3.9.0 2026-04-22 [1] RSPM

promises 1.5.0 2025-11-01 [1] RSPM

ps 1.9.3 2026-04-20 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-05-14 [1] Github (Gilead-BioStats/qcthat@d0958dc)

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Rcpp 1.1.1-1.1 2026-04-24 [1] RSPM

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rmarkdown 2.31 2026-03-26 [1] RSPM

rpart 4.1.27 2026-03-27 [3] CRAN (R 4.6.0)

rprojroot 2.1.1 2025-08-26 [1] RSPM

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[1] /home/runner/work/_temp/Library

[2] /opt/R/4.6.0/lib/R/site-library

[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

@zdz2101 Zelos Zhu (zdz2101) changed the title test: add gh-mocked coverage for snapshot helpers Closes #43 test: add gh-mocked coverage for snapshot helpers May 14, 2026
Copilot AI reviewed May 14, 2026
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Pull request overview

This PR introduces a mockable gh_api() wrapper around gh api calls and adds testthat unit coverage for snapshot helper functions by mocking GitHub CLI responses, addressing the need for defensible testing without hitting the live GitHub API (Closes #43).

Changes:

  • Added internal gh_api() seam and routed GitHub CLI calls in snapshot helper utilities through it.
  • Added mocked testthat coverage for resolve_package(), gh_list_contents(), and pull_workflows() key paths (explicit ref, date fallback, malformed commit lookup, directory parsing, skip/dispatch behavior).

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File Description
R/utils-github.R Introduces gh_api() wrapper and reroutes ref/sha/version GitHub lookups through it for mockability.
R/utils-workflows.R Reroutes workflow content listing and file pulls through gh_api() to enable deterministic tests.
tests/testthat/test-snapshot-gh-mocks.R Adds mocked unit tests covering snapshot helper behaviors without live gh calls.

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Comment thread R/utils-workflows.R Outdated
@zdz2101
Add snapshot orchestration and gh fallback tests
dd498e0 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 15, 2026
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Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

R/utils-workflows.R:61

  • gh_list_contents() combines names/types/paths via mapply() without verifying that the three gh_api(... --jq ...) calls returned the same number of rows (or that types/paths aren’t error strings like "Not Found"). If one jq call fails or returns a different length, mapply() will recycle values and produce incorrect entry mappings. Add an explicit check that length(names) == length(types) && length(types) == length(paths) (and that none contain "Not Found") before constructing entries; otherwise return NULL or raise a clear error.
  if (length(names) == 0) return(NULL)

  mapply(function(n, t, p) list(name = n, type = t, path = p),
         trimws(names), trimws(types), trimws(paths),
         SIMPLIFY = FALSE, USE.NAMES = FALSE)

Comment thread R/utils-github.R
@zdz2101
Mark gh_api roxygen block noRd
da94717 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 15, 2026
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Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated no new comments.

@zdz2101 Zelos Zhu (zdz2101) mentioned this pull request May 15, 2026
Open
@zdz2101
catch up to dev
ec64031 
Merge branch 'dev' into fix-43
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github-actions Bot commented May 15, 2026

✅ All workflows are up to date

Generated by this GitHub Action. Updated: 2026-05-15T18:01:38Z

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github-actions Bot commented May 15, 2026

📊 Test coverage: 45.32%

Per-file coverage
File Coverage
R/DemoApp.R 0%
R/internal.R 75.6%
R/MakeWorkflowList.R 86.1%
R/RunProject.R 90.3%
R/RunQuery.R 90.7%
R/RunStep.R 97.6%
R/RunWorkflow.R 87.5%
R/RunWorkflows.R 100%
R/snapshot.R 85.7%
R/utils-examples.R 95%
R/utils-github.R 63.1%
R/utils-manifest.R 0%
R/utils-toml.R 100%
R/utils-workflows.R 69.4%

Generated by this GitHub Action. Updated: 2026-05-15T18:03:19Z

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github-actions Bot commented May 15, 2026

🌐 PR pkgdown deployed: https://Gilead-BioStats.github.io/workr/pr/48/dev

Generated by this GitHub Action. Updated: 2026-05-15T18:03:34Z

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@jwildfire Jeremy Wildfire (jwildfire) Awaiting requested review from jwildfire

@lauramaxwell Laura Maxwell (lauramaxwell) Awaiting requested review from lauramaxwell

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[workr] Add testthat coverage for pull_workflows and resolve_package

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