From 9c07c3c2a4c83ce6da867e22e2d720f18f59ad6f Mon Sep 17 00:00:00 2001
From: zdz2101 <zelos.zhu@atorusresearch.com>
Date: Thu, 14 May 2026 11:06:47 -0700
Subject: [PATCH 1/3] test: add gh-mocked coverage for snapshot helpers

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 R/utils-github.R                        |  63 +++++----
 R/utils-workflows.R                     |  33 ++---
 tests/testthat/test-snapshot-gh-mocks.R | 167 ++++++++++++++++++++++++
 3 files changed, 211 insertions(+), 52 deletions(-)
 create mode 100644 tests/testthat/test-snapshot-gh-mocks.R

diff --git a/R/utils-github.R b/R/utils-github.R
index f7d5fa6..feebfe9 100644
--- a/R/utils-github.R
+++ b/R/utils-github.R
@@ -55,6 +55,12 @@ resolve_package <- function(org, repo, ref = NULL, date = NULL) {
   )
 }
 
+#' Execute a gh api call and return stdout/stderr lines
+#' @keywords internal
+gh_api <- function(args) {
+  system2("gh", args, stdout = TRUE, stderr = TRUE)
+}
+
 
 #' Resolve a ref by date — find the latest release/tag on or before the given date
 #'
@@ -67,31 +73,27 @@ resolve_ref_by_date <- function(org, repo, date = NULL) {
 
   if (is.null(date)) {
     # Get latest release tag
-    result <- system2(
-      "gh", c("api", paste0("repos/", full_repo, "/releases/latest"), "--jq", ".tag_name"),
-      stdout = TRUE, stderr = TRUE
+    result <- gh_api(
+      c("api", paste0("repos/", full_repo, "/releases/latest"), "--jq", ".tag_name")
     )
     if (length(result) > 0 && !grepl("Not Found", result[1])) {
       return(trimws(result[1]))
     }
     # No releases — fall back to default branch
-    result <- system2(
-      "gh", c("api", paste0("repos/", full_repo), "--jq", ".default_branch"),
-      stdout = TRUE, stderr = TRUE
+    result <- gh_api(
+      c("api", paste0("repos/", full_repo), "--jq", ".default_branch")
     )
     return(trimws(result[1]))
   }
 
   # Get all release tag names and dates separately
-  tags <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/releases"), "--paginate",
-            "--jq", ".[].tag_name"),
-    stdout = TRUE, stderr = TRUE
+  tags <- gh_api(
+    c("api", paste0("repos/", full_repo, "/releases"), "--paginate",
+      "--jq", ".[].tag_name")
   )
-  dates <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/releases"), "--paginate",
-            "--jq", ".[].published_at"),
-    stdout = TRUE, stderr = TRUE
+  dates <- gh_api(
+    c("api", paste0("repos/", full_repo, "/releases"), "--paginate",
+      "--jq", ".[].published_at")
   )
 
   if (length(tags) == 0 || all(grepl("Not Found", tags))) {
@@ -127,10 +129,9 @@ resolve_tag_by_date <- function(org, repo, date) {
   full_repo <- paste0(org, "/", repo)
 
   # Get tags with their commit dates
-  result <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/tags"), "--paginate",
-            "--jq", ".[].name"),
-    stdout = TRUE, stderr = TRUE
+  result <- gh_api(
+    c("api", paste0("repos/", full_repo, "/tags"), "--paginate",
+      "--jq", ".[].name")
   )
 
   if (length(result) == 0) {
@@ -139,16 +140,14 @@ resolve_tag_by_date <- function(org, repo, date) {
 
   # For each tag, get the commit date
   tag_dates <- lapply(result, function(tag) {
-    commit_info <- system2(
-      "gh", c("api", paste0("repos/", full_repo, "/git/ref/tags/", tag),
-              "--jq", ".object.sha"),
-      stdout = TRUE, stderr = TRUE
+    commit_info <- gh_api(
+      c("api", paste0("repos/", full_repo, "/git/ref/tags/", tag),
+        "--jq", ".object.sha")
     )
     sha <- trimws(commit_info[1])
-    commit_date_str <- system2(
-      "gh", c("api", paste0("repos/", full_repo, "/commits/", sha),
-              "--jq", ".commit.committer.date"),
-      stdout = TRUE, stderr = TRUE
+    commit_date_str <- gh_api(
+      c("api", paste0("repos/", full_repo, "/commits/", sha),
+        "--jq", ".commit.committer.date")
     )
     list(tag = tag, date = as.Date(substr(trimws(commit_date_str[1]), 1, 10)))
   })
@@ -172,9 +171,8 @@ resolve_tag_by_date <- function(org, repo, date) {
 #' @return Character. The full commit SHA.
 gh_get_sha <- function(org, repo, ref) {
   full_repo <- paste0(org, "/", repo)
-  result <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/commits/", ref), "--jq", ".sha"),
-    stdout = TRUE, stderr = TRUE
+  result <- gh_api(
+    c("api", paste0("repos/", full_repo, "/commits/", ref), "--jq", ".sha")
   )
   if (length(result) == 0 || grepl("Not Found", result[1])) {
     stop("Could not resolve ref '", ref, "' for ", full_repo)
@@ -190,10 +188,9 @@ gh_get_sha <- function(org, repo, ref) {
 #' @return Character. The package version string.
 gh_get_version <- function(org, repo, sha) {
   full_repo <- paste0(org, "/", repo)
-  result <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/DESCRIPTION?ref=", sha),
-            "--jq", ".content"),
-    stdout = TRUE, stderr = TRUE
+  result <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/DESCRIPTION?ref=", sha),
+      "--jq", ".content")
   )
 
   if (length(result) == 0 || grepl("Not Found", result[1])) {
diff --git a/R/utils-workflows.R b/R/utils-workflows.R
index 6ca322f..3ad4385 100644
--- a/R/utils-workflows.R
+++ b/R/utils-workflows.R
@@ -32,9 +32,8 @@ pull_workflows <- function(resolved, path) {
 #' List contents of a GitHub directory, returning name/type/path for each entry
 #' @keywords internal
 gh_list_contents <- function(full_repo, dir_path, sha) {
-  json_str <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha)),
-    stdout = TRUE, stderr = TRUE
+  json_str <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha))
   )
 
   if (length(json_str) == 0 || any(grepl("Not Found", json_str))) {
@@ -48,20 +47,17 @@ gh_list_contents <- function(full_repo, dir_path, sha) {
 
   # problematic with escaping, parse the raw JSON with a simple approach
   # We'll re-call gh with separate jq queries for each field
-  names <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
-            "--jq", ".[].name"),
-    stdout = TRUE, stderr = TRUE
+  names <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
+      "--jq", ".[].name")
   )
-  types <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
-            "--jq", ".[].type"),
-    stdout = TRUE, stderr = TRUE
+  types <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
+      "--jq", ".[].type")
   )
-  paths <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
-            "--jq", ".[].path"),
-    stdout = TRUE, stderr = TRUE
+  paths <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
+      "--jq", ".[].path")
   )
 
   if (length(names) == 0) return(NULL)
@@ -93,10 +89,9 @@ pull_workflow_dir <- function(full_repo, sha, api_path, local_dir) {
 #' Pull a single workflow file from GitHub
 #' @keywords internal
 pull_workflow_file <- function(full_repo, sha, api_path, local_path) {
-  file_content <- system2(
-    "gh", c("api", paste0("repos/", full_repo, "/contents/", api_path, "?ref=", sha),
-            "--jq", ".content"),
-    stdout = TRUE, stderr = TRUE
+  file_content <- gh_api(
+    c("api", paste0("repos/", full_repo, "/contents/", api_path, "?ref=", sha),
+      "--jq", ".content")
   )
 
   if (length(file_content) > 0 && !any(grepl("Not Found", file_content))) {
diff --git a/tests/testthat/test-snapshot-gh-mocks.R b/tests/testthat/test-snapshot-gh-mocks.R
new file mode 100644
index 0000000..66506bd
--- /dev/null
+++ b/tests/testthat/test-snapshot-gh-mocks.R
@@ -0,0 +1,167 @@
+test_that("resolve_package resolves explicit refs via mocked gh api", {
+  local_mocked_bindings(
+    gh_api = function(args) {
+      cmd <- paste(args, collapse = " ")
+      if (grepl("/commits/v1.2.3", cmd, fixed = TRUE) && grepl(".sha", cmd, fixed = TRUE)) {
+        return("abc123")
+      }
+      if (grepl("contents/DESCRIPTION?ref=abc123", cmd, fixed = TRUE) && grepl(".content", cmd, fixed = TRUE)) {
+        desc <- "Package: gsm.core\nVersion: 1.9.0\n"
+        return(base64enc::base64encode(charToRaw(desc)))
+      }
+      stop("Unexpected gh_api args: ", cmd)
+    },
+    .package = "workr"
+  )
+
+  out <- workr:::resolve_package("Gilead-BioStats", "gsm.core", ref = "v1.2.3")
+  expect_equal(out$org, "Gilead-BioStats")
+  expect_equal(out$repo, "gsm.core")
+  expect_equal(out$ref, "v1.2.3")
+  expect_equal(out$sha, "abc123")
+  expect_equal(out$version, "1.9.0")
+})
+
+test_that("resolve_package uses date-based fallback when ref is not provided", {
+  local_mocked_bindings(
+    gh_api = function(args) {
+      cmd <- paste(args, collapse = " ")
+      if (grepl("/releases --paginate --jq .\\[\\]\\.tag_name", cmd)) {
+        return(c("v1.0.0", "v1.1.0"))
+      }
+      if (grepl("/releases --paginate --jq .\\[\\]\\.published_at", cmd)) {
+        return(c("2024-01-15T00:00:00Z", "2024-06-15T00:00:00Z"))
+      }
+      if (grepl("/commits/v1.0.0", cmd, fixed = TRUE) && grepl(".sha", cmd, fixed = TRUE)) {
+        return("sha-v1-0-0")
+      }
+      if (grepl("contents/DESCRIPTION?ref=sha-v1-0-0", cmd, fixed = TRUE) && grepl(".content", cmd, fixed = TRUE)) {
+        desc <- "Package: gsm.core\nVersion: 1.0.0\n"
+        return(base64enc::base64encode(charToRaw(desc)))
+      }
+      stop("Unexpected gh_api args: ", cmd)
+    },
+    .package = "workr"
+  )
+
+  out <- workr:::resolve_package(
+    org = "Gilead-BioStats",
+    repo = "gsm.core",
+    ref = NULL,
+    date = as.Date("2024-05-01")
+  )
+
+  expect_equal(out$ref, "v1.0.0")
+  expect_equal(out$sha, "sha-v1-0-0")
+  expect_equal(out$version, "1.0.0")
+})
+
+test_that("resolve_package errors on malformed gh commit lookup response", {
+  local_mocked_bindings(
+    gh_api = function(args) {
+      cmd <- paste(args, collapse = " ")
+      if (grepl("/commits/dev", cmd, fixed = TRUE) && grepl(".sha", cmd, fixed = TRUE)) {
+        return("Not Found")
+      }
+      stop("Unexpected gh_api args: ", cmd)
+    },
+    .package = "workr"
+  )
+
+  expect_error(
+    workr:::resolve_package("Gilead-BioStats", "gsm.core", ref = "dev"),
+    "Could not resolve ref"
+  )
+})
+
+test_that("gh_list_contents parses directory entries from mocked gh api", {
+  local_mocked_bindings(
+    gh_api = function(args) {
+      cmd <- paste(args, collapse = " ")
+      if (!("--jq" %in% args)) {
+        return("[]")
+      }
+      if (grepl(".[].name", cmd, fixed = TRUE)) {
+        return(c("0_other", "foo.yaml"))
+      }
+      if (grepl(".[].type", cmd, fixed = TRUE)) {
+        return(c("dir", "file"))
+      }
+      if (grepl(".[].path", cmd, fixed = TRUE)) {
+        return(c("inst/workflow/0_other", "inst/workflow/foo.yaml"))
+      }
+      stop("Unexpected gh_api args: ", cmd)
+    },
+    .package = "workr"
+  )
+
+  entries <- workr:::gh_list_contents("Gilead-BioStats/gsm.core", "inst/workflow", "abc123")
+  expect_length(entries, 2)
+  expect_equal(entries[[1]]$name, "0_other")
+  expect_equal(entries[[1]]$type, "dir")
+  expect_equal(entries[[2]]$name, "foo.yaml")
+  expect_equal(entries[[2]]$type, "file")
+})
+
+test_that("pull_workflows skips packages with no workflow directory", {
+  tmp <- tempfile("workr-pull-workflows-")
+  dir.create(tmp, recursive = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE), add = TRUE)
+
+  local_mocked_bindings(
+    gh_list_contents = function(full_repo, dir_path, sha) {
+      NULL
+    },
+    .package = "workr"
+  )
+
+  resolved <- list(list(org = "Gilead-BioStats", repo = "gsm.core", sha = "abc123"))
+  expect_message(
+    workr:::pull_workflows(resolved, tmp),
+    "No inst/workflow found"
+  )
+  expect_true(dir.exists(file.path(tmp, "workflows")))
+})
+
+test_that("pull_workflows dispatches file and directory entries", {
+  tmp <- tempfile("workr-pull-workflows-")
+  dir.create(tmp, recursive = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE), add = TRUE)
+
+  dir_calls <- character()
+  file_calls <- character()
+
+  local_mocked_bindings(
+    gh_list_contents = function(full_repo, dir_path, sha) {
+      list(
+        list(type = "dir", name = "0_other", path = "inst/workflow/0_other"),
+        list(type = "file", name = "root.yaml", path = "inst/workflow/root.yaml")
+      )
+    },
+    pull_workflow_dir = function(full_repo, sha, api_path, local_dir) {
+      dir_calls <<- c(dir_calls, paste(full_repo, sha, api_path, local_dir, sep = "|"))
+      invisible(NULL)
+    },
+    pull_workflow_file = function(full_repo, sha, api_path, local_path) {
+      file_calls <<- c(file_calls, paste(full_repo, sha, api_path, local_path, sep = "|"))
+      invisible(NULL)
+    },
+    .package = "workr"
+  )
+
+  resolved <- list(list(org = "Gilead-BioStats", repo = "gsm.core", sha = "abc123"))
+  workr:::pull_workflows(resolved, tmp)
+
+  expect_length(dir_calls, 1)
+  expect_length(file_calls, 1)
+  dir_parts <- strsplit(dir_calls[[1]], "|", fixed = TRUE)[[1]]
+  file_parts <- strsplit(file_calls[[1]], "|", fixed = TRUE)[[1]]
+  expect_equal(dir_parts[1], "Gilead-BioStats/gsm.core")
+  expect_equal(dir_parts[2], "abc123")
+  expect_equal(dir_parts[3], "inst/workflow/0_other")
+  expect_equal(basename(dir_parts[4]), "0_other")
+  expect_equal(file_parts[1], "Gilead-BioStats/gsm.core")
+  expect_equal(file_parts[2], "abc123")
+  expect_equal(file_parts[3], "inst/workflow/root.yaml")
+  expect_equal(basename(file_parts[4]), "root.yaml")
+})

From dd498e0edcac1a9d9a036f883f2c106f65686434 Mon Sep 17 00:00:00 2001
From: zdz2101 <zelos.zhu@atorusresearch.com>
Date: Fri, 15 May 2026 08:34:55 -0700
Subject: [PATCH 2/3] Add snapshot orchestration and gh fallback tests

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 R/utils-workflows.R                     |   8 +-
 tests/testthat/test-snapshot-gh-mocks.R | 105 ++++++++++++++++++++++++
 2 files changed, 106 insertions(+), 7 deletions(-)

diff --git a/R/utils-workflows.R b/R/utils-workflows.R
index 3ad4385..a7a3753 100644
--- a/R/utils-workflows.R
+++ b/R/utils-workflows.R
@@ -40,13 +40,7 @@ gh_list_contents <- function(full_repo, dir_path, sha) {
     return(NULL)
   }
 
-  # Minimal JSON parsing — extract name, type, path from each object
-  json_text <- paste0(json_str, collapse = "\n")
-
-  # Use R's built-in JSON-ish parsing via the gh CLI --jq, but since that's
-
-  # problematic with escaping, parse the raw JSON with a simple approach
-  # We'll re-call gh with separate jq queries for each field
+  # Re-call gh with separate jq queries for each field.
   names <- gh_api(
     c("api", paste0("repos/", full_repo, "/contents/", dir_path, "?ref=", sha),
       "--jq", ".[].name")
diff --git a/tests/testthat/test-snapshot-gh-mocks.R b/tests/testthat/test-snapshot-gh-mocks.R
index 66506bd..7a72383 100644
--- a/tests/testthat/test-snapshot-gh-mocks.R
+++ b/tests/testthat/test-snapshot-gh-mocks.R
@@ -74,6 +74,25 @@ test_that("resolve_package errors on malformed gh commit lookup response", {
   )
 })
 
+test_that("resolve_ref_by_date falls back to default branch when latest release is missing", {
+  local_mocked_bindings(
+    gh_api = function(args) {
+      cmd <- paste(args, collapse = " ")
+      if (grepl("/releases/latest", cmd, fixed = TRUE) && grepl(".tag_name", cmd, fixed = TRUE)) {
+        return("Not Found")
+      }
+      if (grepl("repos/Gilead-BioStats/gsm.core --jq .default_branch", cmd, fixed = TRUE)) {
+        return("main")
+      }
+      stop("Unexpected gh_api args: ", cmd)
+    },
+    .package = "workr"
+  )
+
+  out <- workr:::resolve_ref_by_date("Gilead-BioStats", "gsm.core", date = NULL)
+  expect_equal(out, "main")
+})
+
 test_that("gh_list_contents parses directory entries from mocked gh api", {
   local_mocked_bindings(
     gh_api = function(args) {
@@ -103,6 +122,49 @@ test_that("gh_list_contents parses directory entries from mocked gh api", {
   expect_equal(entries[[2]]$type, "file")
 })
 
+test_that("pkgManifest writes manifest outputs with mocked GitHub resolution", {
+  tmp <- tempfile("workr-pkg-manifest-")
+  dir.create(tmp, recursive = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE), add = TRUE)
+
+  resolve_calls <- list()
+
+  local_mocked_bindings(
+    resolve_package = function(org, repo, ref = NULL, date = NULL) {
+      resolve_calls <<- append(resolve_calls, list(list(org = org, repo = repo, ref = ref, date = date)))
+      list(
+        org = org,
+        repo = repo,
+        version = "1.0.0",
+        repository = paste0("https://github.com/", org, "/", repo),
+        url = paste0("https://github.com/", org, "/", repo, "/archive/sha-", repo, ".tar.gz"),
+        sha = paste0("sha-", repo),
+        ref = ref
+      )
+    },
+    pull_workflows = function(resolved, path) {
+      dir.create(file.path(path, "workflows"), recursive = TRUE, showWarnings = FALSE)
+      writeLines("name: mocked-workflow", file.path(path, "workflows", "root.yaml"))
+      invisible(NULL)
+    },
+    .package = "workr"
+  )
+
+  out <- workr::pkgManifest(
+    path = tmp,
+    packageList = c("Gilead-BioStats/gsm.core@v1.2.3", "Gilead-BioStats/gsm.mapping"),
+    branch = "dev"
+  )
+
+  expect_true(file.exists(file.path(tmp, "manifest.csv")))
+  expect_true(file.exists(file.path(tmp, "rproject.toml")))
+  expect_true(file.exists(file.path(tmp, "workflows", "root.yaml")))
+  expect_equal(nrow(out), 2)
+  expect_equal(out$package, c("gsm.core", "gsm.mapping"))
+  expect_equal(resolve_calls[[1]]$ref, "v1.2.3")
+  expect_equal(resolve_calls[[2]]$ref, "dev")
+})
+
 test_that("pull_workflows skips packages with no workflow directory", {
   tmp <- tempfile("workr-pull-workflows-")
   dir.create(tmp, recursive = TRUE)
@@ -165,3 +227,46 @@ test_that("pull_workflows dispatches file and directory entries", {
   expect_equal(file_parts[3], "inst/workflow/root.yaml")
   expect_equal(basename(file_parts[4]), "root.yaml")
 })
+
+test_that("pull_workflow_file skips write when content lookup is Not Found", {
+  tmp <- tempfile("workr-pull-workflow-file-")
+  on.exit(unlink(tmp, force = TRUE), add = TRUE)
+
+  local_mocked_bindings(
+    gh_api = function(args) {
+      "Not Found"
+    },
+    .package = "workr"
+  )
+
+  workr:::pull_workflow_file(
+    full_repo = "Gilead-BioStats/gsm.core",
+    sha = "abc123",
+    api_path = "inst/workflow/root.yaml",
+    local_path = tmp
+  )
+
+  expect_false(file.exists(tmp))
+})
+
+test_that("pull_workflow_file writes decoded file when content is available", {
+  tmp <- tempfile("workr-pull-workflow-file-")
+  on.exit(unlink(tmp, force = TRUE), add = TRUE)
+
+  local_mocked_bindings(
+    gh_api = function(args) {
+      base64enc::base64encode(charToRaw("name: workflow\n"))
+    },
+    .package = "workr"
+  )
+
+  workr:::pull_workflow_file(
+    full_repo = "Gilead-BioStats/gsm.core",
+    sha = "abc123",
+    api_path = "inst/workflow/root.yaml",
+    local_path = tmp
+  )
+
+  expect_true(file.exists(tmp))
+  expect_identical(readLines(tmp)[1], "name: workflow")
+})

From da94717d433ab511b32ee6842d967b1e1f81912c Mon Sep 17 00:00:00 2001
From: zdz2101 <zelos.zhu@atorusresearch.com>
Date: Fri, 15 May 2026 08:46:34 -0700
Subject: [PATCH 3/3] Mark gh_api roxygen block noRd

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 R/utils-github.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/utils-github.R b/R/utils-github.R
index feebfe9..ff80792 100644
--- a/R/utils-github.R
+++ b/R/utils-github.R
@@ -57,6 +57,7 @@ resolve_package <- function(org, repo, ref = NULL, date = NULL) {
 
 #' Execute a gh api call and return stdout/stderr lines
 #' @keywords internal
+#' @noRd
 gh_api <- function(args) {
   system2("gh", args, stdout = TRUE, stderr = TRUE)
 }