From 7b3647b7e07b36653bdd984f582d6c7b10f40684 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Thu, 22 Feb 2024 17:35:31 +0000
Subject: [PATCH 01/10] Add endpoint to list reports on a branch

---
 .Rbuildignore                                |  2 +
 DESCRIPTION                                  |  3 +-
 R/api.R                                      | 15 +++++-
 R/git.R                                      | 37 +++++++++++++
 R/porcelain.R                                | 10 ++++
 R/util.R                                     | 24 +++++++++
 R/util_assert.R                              | 23 ++++++++
 inst/schema/report_list.json                 | 10 ++++
 orderly.runner.Rproj                         | 17 ++++++
 tests/testthat/examples/data/orderly.R       |  3 ++
 tests/testthat/examples/parameters/orderly.R |  2 +
 tests/testthat/helper-orderly-runner.R       | 57 ++++++++++++++++++++
 tests/testthat/test-api.R                    | 31 +++++++++++
 tests/testthat/test-git.R                    | 48 +++++++++++++++++
 tests/testthat/test-util-assert.R            | 12 +++++
 15 files changed, 292 insertions(+), 2 deletions(-)
 create mode 100644 R/git.R
 create mode 100644 R/util_assert.R
 create mode 100644 inst/schema/report_list.json
 create mode 100644 orderly.runner.Rproj
 create mode 100644 tests/testthat/examples/data/orderly.R
 create mode 100644 tests/testthat/examples/parameters/orderly.R
 create mode 100644 tests/testthat/test-git.R
 create mode 100644 tests/testthat/test-util-assert.R

diff --git a/.Rbuildignore b/.Rbuildignore
index 1212a32..baae540 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -21,3 +21,5 @@
 ^\.covrignore$
 ^\.github$
 \.*gcov$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/DESCRIPTION b/DESCRIPTION
index 59530b5..10b2341 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,12 +8,13 @@ Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
 Description: Small HTTP server for running orderly reports.
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "porcelain::porcelain_roclet"))
 URL: https://github.com/mrc-ide/orderly.runner
 BugReports: https://github.com/mrc-ide/orderly.runner/issues
 Imports:
     docopt,
+    gert,
     jsonlite,
     orderly2,
     porcelain,
diff --git a/R/api.R b/R/api.R
index 14d3fb7..382264e 100644
--- a/R/api.R
+++ b/R/api.R
@@ -16,7 +16,6 @@
 ##'
 ##' @export
 api <- function(root, validate = NULL, log_level = "info") {
-  orderly2::orderly_list_src(root, locate = FALSE)
   logger <- porcelain::porcelain_logger(log_level)
   api <- porcelain::porcelain$new(validate = validate, logger = logger)
   api$include_package_endpoints(state = list(root = root))
@@ -30,3 +29,17 @@ root <- function() {
                    orderly.runner = package_version_string("orderly.runner"))
   lapply(versions, scalar)
 }
+
+##' @porcelain 
+##'   GET /report/list => json(report_list)
+##'   query hash :: string
+##'   state root :: root
+report_list <- function(root, hash) {
+  temp_root <- git_clone_depth_1(root, hash)
+  src_reports <- orderly2::orderly_list_src(temp_root, locate = FALSE)
+  lapply(src_reports, function(report_name) {
+    list(
+      name = scalar(report_name)
+    )
+  })
+}
diff --git a/R/git.R b/R/git.R
new file mode 100644
index 0000000..29d0971
--- /dev/null
+++ b/R/git.R
@@ -0,0 +1,37 @@
+git_run <- function(args, repo = NULL, check = FALSE) {
+  git <- sys_which("git")
+  if (!is.null(repo)) {
+    args <- c("-C", repo, args)
+  }
+  res <- system3(git, args)
+  if (check && !res$success) {
+    stop(sprintf("Error code %d running command:\n%s",
+                 res$code, paste0("  > ", res$output, collapse = "\n")))
+  }
+  res
+}
+
+
+git_ref_to_sha <- function(ref, repo = NULL, check = FALSE) {
+  assert_scalar_character(ref)
+  res <- git_run(c("rev-parse", ref), repo = repo, check = FALSE)
+  if (res$success) {
+    res$output
+  } else if (check) {
+    stop(sprintf("Git reference '%s' not found", ref), call. = FALSE)
+  } else {
+    NA_character_
+  }
+}
+
+
+git_clone_depth_1 <- function(origin, ref) {
+  t <- tempfile()
+  dir.create(t)
+  gert::git_init(t)
+  gert::git_remote_add(origin, repo = t)
+  sha <- git_ref_to_sha(ref, repo = origin, check = TRUE)
+  git_run(c("fetch", "--depth", "1", "origin", sha), repo = t)
+  git_run(c("checkout", "FETCH_HEAD"), repo = t)
+  t
+}
diff --git a/R/porcelain.R b/R/porcelain.R
index 4381491..e290b13 100644
--- a/R/porcelain.R
+++ b/R/porcelain.R
@@ -8,5 +8,15 @@
         root,
         returning = porcelain::porcelain_returning_json("root"),
         validate = validate)
+    },
+    "GET /report/list" = function(state, validate) {
+      porcelain::porcelain_endpoint$new(
+        "GET",
+        "/report/list",
+        report_list,
+        porcelain::porcelain_input_query(hash = "string"),
+        porcelain::porcelain_state(root = state$root),
+        returning = porcelain::porcelain_returning_json("report_list"),
+        validate = validate)
     })
 }
diff --git a/R/util.R b/R/util.R
index e376947..d04efe5 100644
--- a/R/util.R
+++ b/R/util.R
@@ -11,3 +11,27 @@ scalar <- function(x) {
 package_version_string <- function(name) {
   as.character(utils::packageVersion(name))
 }
+
+
+system3 <- function(command, args) {
+  res <- suppressWarnings(system2(command, args, stdout = TRUE, stderr = TRUE))
+  code <- attr(res, "status") %||% 0
+  attr(res, "status") <- NULL
+  list(success = code == 0,
+       code = code,
+       output = res)
+}
+
+
+sys_which <- function(name) {
+  path <- Sys.which(name)
+  if (!nzchar(path)) {
+    stop(sprintf("Did not find '%s'", name), call. = FALSE)
+  }
+  unname(path)
+}
+
+
+vcapply <- function(X, FUN, ...) { # nolint
+  vapply(X, FUN, character(1), ...)
+}
diff --git a/R/util_assert.R b/R/util_assert.R
new file mode 100644
index 0000000..93ec841
--- /dev/null
+++ b/R/util_assert.R
@@ -0,0 +1,23 @@
+assert_scalar <- function(x, name = deparse(substitute(x)), arg = name,
+                          call = NULL) {
+  if (length(x) != 1) {
+    cli::cli_abort(c("'{name}' must be a scalar",
+                     i = "{name} has length {length(x)}"),
+                   call = call, arg = arg)
+  }
+}
+
+
+assert_character <- function(x, name = deparse(substitute(x)),
+                             arg = name, call = NULL) {
+  if (!is.character(x)) {
+    cli::cli_abort("'{name}' must be character", call = call, arg = arg)
+  }
+}
+
+
+assert_scalar_character <- function(x, name = deparse(substitute(x)),
+                                    arg = name, call = NULL) {
+  assert_scalar(x, name, arg = arg, call = call)
+  assert_character(x, name, arg = arg, call = call)
+}
diff --git a/inst/schema/report_list.json b/inst/schema/report_list.json
new file mode 100644
index 0000000..9b9bdbc
--- /dev/null
+++ b/inst/schema/report_list.json
@@ -0,0 +1,10 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "type": "array",
+    "items": {
+      "type": "object",
+      "properties": {
+        "name": { "type": "string" }
+      }
+    }
+}
diff --git a/orderly.runner.Rproj b/orderly.runner.Rproj
new file mode 100644
index 0000000..21a4da0
--- /dev/null
+++ b/orderly.runner.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/tests/testthat/examples/data/orderly.R b/tests/testthat/examples/data/orderly.R
new file mode 100644
index 0000000..c7a6add
--- /dev/null
+++ b/tests/testthat/examples/data/orderly.R
@@ -0,0 +1,3 @@
+orderly2::orderly_artefact("Some data", "data.rds")
+d <- data.frame(a = 1:10, x = runif(10), y = 1:10 + runif(10))
+saveRDS(d, "data.rds")
diff --git a/tests/testthat/examples/parameters/orderly.R b/tests/testthat/examples/parameters/orderly.R
new file mode 100644
index 0000000..ecdcd5b
--- /dev/null
+++ b/tests/testthat/examples/parameters/orderly.R
@@ -0,0 +1,2 @@
+orderly2::orderly_parameters(a = NULL, b = 2, c = NULL)
+saveRDS(list(a = a, b = b, c = c), "data.rds")
diff --git a/tests/testthat/helper-orderly-runner.R b/tests/testthat/helper-orderly-runner.R
index 9495802..c2899d2 100644
--- a/tests/testthat/helper-orderly-runner.R
+++ b/tests/testthat/helper-orderly-runner.R
@@ -10,3 +10,60 @@ create_temporary_root <- function(...) {
   withr::defer_parent(unlink(path, recursive = TRUE))
   suppressMessages(orderly2::orderly_init(path, ...))
 }
+
+
+test_prepare_orderly_example <- function(examples, ...) {
+  tmp <- tempfile()
+  withr::defer_parent(unlink(tmp, recursive = TRUE))
+  suppressMessages(orderly2::orderly_init(tmp, ...))
+  copy_examples(examples, tmp)
+  as.character(fs::path_norm(tmp))
+}
+
+
+copy_examples <- function(examples, path_src) {
+  fs::dir_create(path_src)
+
+  fs::dir_create(file.path(path_src, "src"))
+  for (i in examples) {
+    fs::dir_copy(test_path("examples", i), file.path(path_src, "src"))
+  }
+}
+
+
+helper_add_git <- function(path) {
+  gert::git_init(path)
+  gert::git_add(".", repo = path)
+  user <- "author <author@example.com>"
+  sha <- gert::git_commit("initial", author = user, committer = user,
+                          repo = path)
+  branch <- gert::git_branch(repo = path)
+  url <- "https://example.com/git"
+  gert::git_remote_add(url, repo = path)
+  list(path = path, user = user, branch = branch, sha = sha, url = url)
+}
+
+
+initialise_git_repo <- function() {
+  t <- tempfile()
+  dir.create(t)
+  writeLines(c("# Example", "", "example repo"), file.path(t, "README.md"))
+  helper_add_git(t)
+}
+
+
+create_new_commit <- function(path, new_file = "new", message = "new message") {
+  writeLines("new file", file.path(path, new_file))
+  gert::git_add(".", repo = path)
+  user <- "author <author@example.com>"
+  gert::git_commit(message, author = user, committer = user, repo = path)
+}
+
+
+create_new_branch <- function(path, branch_name = "other") {
+  initial_branch <- gert::git_branch(repo = path)
+  gert::git_branch_create(branch_name, repo = path)
+  commit_sha <- create_new_commit(path, branch_name)
+  gert::git_branch_checkout(initial_branch, repo = path)
+  list(branch = branch_name, sha = commit_sha)
+}
diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index f2d9155..28c8410 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -18,3 +18,34 @@ test_that("Can construct the api", {
   expect_length(logs, 2)
   expect_equal(logs[[1]]$logger, "orderly.runner")
 })
+
+
+test_that("can list orderly reports", {
+  path <- test_prepare_orderly_example(c("data", "parameters"))
+  repo <- helper_add_git(path)
+  endpoint <- orderly_runner_endpoint("GET", "/report/list", path)
+  get_reports_from_response <- function(res) {
+    vcapply(res$data, function(item) as.character(item[["name"]]))
+  }
+
+  res <- endpoint$run("main")
+  expect_equal(res$status_code, 200)
+  expect_setequal(get_reports_from_response(res), c("data", "parameters"))
+
+  ## Delete a report on a 2nd branch
+  gert::git_branch_create("other", repo = path)
+  unlink(file.path(path, "src", "data"), recursive = TRUE)
+  gert::git_add(".", repo = path)
+  sha <- gert::git_commit("Remove data report", repo = path)
+
+  ## Can list items from this sha
+  other_res <- endpoint$run(sha)
+  expect_equal(other_res$status_code, 200)
+  expect_equal(get_reports_from_response(other_res), "parameters")
+
+  ## We can still see all reports on main branch
+  first_commit_res <- endpoint$run(repo$sha)
+  expect_equal(first_commit_res$status_code, 200)
+  expect_setequal(get_reports_from_response(first_commit_res), 
+                  c("data", "parameters"))
+})
diff --git a/tests/testthat/test-git.R b/tests/testthat/test-git.R
new file mode 100644
index 0000000..3e7f3f6
--- /dev/null
+++ b/tests/testthat/test-git.R
@@ -0,0 +1,48 @@
+test_that("can do depth 1 clone", {
+  repo <- initialise_git_repo()
+  
+  first_commit <- repo$sha
+  second_commit <- create_new_commit(repo$path)
+  
+  first_clone <- git_clone_depth_1(repo$path, first_commit)
+  log <- gert::git_log(repo = first_clone)
+  expect_true(nrow(log) == 1)
+  expect_equal(log$commit, first_commit)
+  
+  second_clone <- git_clone_depth_1(repo$path, second_commit)
+  log <- gert::git_log(repo = second_clone)
+  expect_true(nrow(log) == 1)
+  expect_equal(log$commit, second_commit)
+})
+
+
+test_that("git ref to sha", {
+  testthat::skip_on_cran()
+  repo <- initialise_git_repo()
+  other <- create_new_branch(repo$path, "other")
+  sha1 <- git_ref_to_sha("main", repo$path)
+  sha2 <- git_ref_to_sha("other", repo$path)
+  
+  expect_match(sha1, "^[[:xdigit:]]{40}$")
+  expect_match(sha2, "^[[:xdigit:]]{40}$")
+  expect_true(sha1 != sha2)
+  
+  expect_equal(git_ref_to_sha("HEAD", repo$path), sha1)
+  expect_equal(git_ref_to_sha(substr(sha1, 1, 7), repo$path), sha1)
+  
+  expect_identical(git_ref_to_sha("unknown", repo$path),
+                   NA_character_)
+  expect_error(git_ref_to_sha("unknown", repo$path, TRUE),
+               "Git reference 'unknown' not found")
+})
+
+
+test_that("handle failure", {
+  testthat::skip_on_cran()
+  repo <- initialise_git_repo()
+  r <- git_run("unknown-command", repo = repo$path)
+  expect_false(r$success)
+  expect_error(
+    git_run("unknown-command", repo = repo$path, check = TRUE),
+    r$output, fixed = TRUE)
+})
diff --git a/tests/testthat/test-util-assert.R b/tests/testthat/test-util-assert.R
new file mode 100644
index 0000000..73d9105
--- /dev/null
+++ b/tests/testthat/test-util-assert.R
@@ -0,0 +1,12 @@
+test_that("assert_scalar", {
+  expect_error(assert_scalar(NULL), "must be a scalar")
+  expect_error(assert_scalar(numeric(0)), "must be a scalar")
+  expect_error(assert_scalar(1:2), "must be a scalar")
+})
+
+
+test_that("assert_character", {
+  expect_silent(assert_character("a"))
+  expect_error(assert_character(1), "must be character")
+  expect_error(assert_character(TRUE), "must be character")
+})

From efa71bf05e136d3725a72590bc1caae122241de2 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Thu, 22 Feb 2024 17:43:52 +0000
Subject: [PATCH 02/10] Add missing imports

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 10b2341..b726445 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,12 +13,14 @@ Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "porcelain::porcel
 URL: https://github.com/mrc-ide/orderly.runner
 BugReports: https://github.com/mrc-ide/orderly.runner/issues
 Imports:
+    cli,
     docopt,
     gert,
     jsonlite,
     orderly2,
     porcelain,
 Suggests:
+    fs,
     httr,
     lgr,
     mockery,

From d1e0a042b4281675911687561c73c4fef355f199 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Thu, 22 Feb 2024 17:46:06 +0000
Subject: [PATCH 03/10] Add author for git commit

---
 tests/testthat/test-api.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index 28c8410..e85d893 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -36,7 +36,8 @@ test_that("can list orderly reports", {
   gert::git_branch_create("other", repo = path)
   unlink(file.path(path, "src", "data"), recursive = TRUE)
   gert::git_add(".", repo = path)
-  sha <- gert::git_commit("Remove data report", repo = path)
+  sha <- gert::git_commit("Remove data report", repo = path,
+                          author = "Test User <test.user@example.com>")
 
   ## Can list items from this sha
   other_res <- endpoint$run(sha)

From 1ca6a3f0652857419b0ff7e11a0e5f90b6babebf Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Thu, 22 Feb 2024 17:55:45 +0000
Subject: [PATCH 04/10] Don't explicitly refer to default branch

Use value returned from test setup to avoid issues with master/main from config differences between local and CI
---
 tests/testthat/test-api.R | 2 +-
 tests/testthat/test-git.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index e85d893..fcc69a6 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -28,7 +28,7 @@ test_that("can list orderly reports", {
     vcapply(res$data, function(item) as.character(item[["name"]]))
   }
 
-  res <- endpoint$run("main")
+  res <- endpoint$run(repo$branch)
   expect_equal(res$status_code, 200)
   expect_setequal(get_reports_from_response(res), c("data", "parameters"))
 
diff --git a/tests/testthat/test-git.R b/tests/testthat/test-git.R
index 3e7f3f6..eda36b3 100644
--- a/tests/testthat/test-git.R
+++ b/tests/testthat/test-git.R
@@ -20,7 +20,7 @@ test_that("git ref to sha", {
   testthat::skip_on_cran()
   repo <- initialise_git_repo()
   other <- create_new_branch(repo$path, "other")
-  sha1 <- git_ref_to_sha("main", repo$path)
+  sha1 <- git_ref_to_sha(repo$branch, repo$path)
   sha2 <- git_ref_to_sha("other", repo$path)
   
   expect_match(sha1, "^[[:xdigit:]]{40}$")

From c4f1ddb3257b50411e94b2f383b551b4b1e1f2ff Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Fri, 23 Feb 2024 14:38:00 +0000
Subject: [PATCH 05/10] Remove git shallow checkout and unused utils and
 helpers

---
 R/api.R                                       | 17 ++++---
 R/git.R                                       | 37 --------------
 R/util.R                                      | 22 ++-------
 R/util_assert.R                               | 23 ---------
 inst/schema/report_list.json                  |  3 +-
 .../examples/data/{orderly.R => data.R}       |  0
 tests/testthat/helper-orderly-runner.R        | 25 ----------
 tests/testthat/test-api.R                     | 12 ++---
 tests/testthat/test-git.R                     | 48 -------------------
 tests/testthat/test-util-assert.R             | 12 -----
 10 files changed, 22 insertions(+), 177 deletions(-)
 delete mode 100644 R/git.R
 delete mode 100644 R/util_assert.R
 rename tests/testthat/examples/data/{orderly.R => data.R} (100%)
 delete mode 100644 tests/testthat/test-git.R
 delete mode 100644 tests/testthat/test-util-assert.R

diff --git a/R/api.R b/R/api.R
index 382264e..660c590 100644
--- a/R/api.R
+++ b/R/api.R
@@ -35,11 +35,14 @@ root <- function() {
 ##'   query hash :: string
 ##'   state root :: root
 report_list <- function(root, hash) {
-  temp_root <- git_clone_depth_1(root, hash)
-  src_reports <- orderly2::orderly_list_src(temp_root, locate = FALSE)
-  lapply(src_reports, function(report_name) {
-    list(
-      name = scalar(report_name)
-    )
-  })
+  contents <- gert::git_ls(root, ref = hash)
+  re <- "^src/([^/]+)/(\\1|orderly)\\.(yml|R)$"
+  nms <- sub(re, "\\1", 
+             grep(re, contents$path, value = TRUE, perl = TRUE), 
+             perl = TRUE)
+  last_changed <- function(nm) {
+    max(contents$modified[startsWith(contents$path, sprintf("src/%s", nm))])
+  }
+  data.frame(name = nms, 
+             updated = vnapply(nms, last_changed, USE.NAMES = FALSE))
 }
diff --git a/R/git.R b/R/git.R
deleted file mode 100644
index 29d0971..0000000
--- a/R/git.R
+++ /dev/null
@@ -1,37 +0,0 @@
-git_run <- function(args, repo = NULL, check = FALSE) {
-  git <- sys_which("git")
-  if (!is.null(repo)) {
-    args <- c("-C", repo, args)
-  }
-  res <- system3(git, args)
-  if (check && !res$success) {
-    stop(sprintf("Error code %d running command:\n%s",
-                 res$code, paste0("  > ", res$output, collapse = "\n")))
-  }
-  res
-}
-
-
-git_ref_to_sha <- function(ref, repo = NULL, check = FALSE) {
-  assert_scalar_character(ref)
-  res <- git_run(c("rev-parse", ref), repo = repo, check = FALSE)
-  if (res$success) {
-    res$output
-  } else if (check) {
-    stop(sprintf("Git reference '%s' not found", ref), call. = FALSE)
-  } else {
-    NA_character_
-  }
-}
-
-
-git_clone_depth_1 <- function(origin, ref) {
-  t <- tempfile()
-  dir.create(t)
-  gert::git_init(t)
-  gert::git_remote_add(origin, repo = t)
-  sha <- git_ref_to_sha(ref, repo = origin, check = TRUE)
-  git_run(c("fetch", "--depth", "1", "origin", sha), repo = t)
-  git_run(c("checkout", "FETCH_HEAD"), repo = t)
-  t
-}
diff --git a/R/util.R b/R/util.R
index d04efe5..9919c03 100644
--- a/R/util.R
+++ b/R/util.R
@@ -13,25 +13,11 @@ package_version_string <- function(name) {
 }
 
 
-system3 <- function(command, args) {
-  res <- suppressWarnings(system2(command, args, stdout = TRUE, stderr = TRUE))
-  code <- attr(res, "status") %||% 0
-  attr(res, "status") <- NULL
-  list(success = code == 0,
-       code = code,
-       output = res)
-}
-
-
-sys_which <- function(name) {
-  path <- Sys.which(name)
-  if (!nzchar(path)) {
-    stop(sprintf("Did not find '%s'", name), call. = FALSE)
-  }
-  unname(path)
+vcapply <- function(X, FUN, ...) { # nolint
+  vapply(X, FUN, character(1), ...)
 }
 
 
-vcapply <- function(X, FUN, ...) { # nolint
-  vapply(X, FUN, character(1), ...)
+vnapply <- function(X, FUN, ...) { # nolint
+  vapply(X, FUN, numeric(1), ...)
 }
diff --git a/R/util_assert.R b/R/util_assert.R
deleted file mode 100644
index 93ec841..0000000
--- a/R/util_assert.R
+++ /dev/null
@@ -1,23 +0,0 @@
-assert_scalar <- function(x, name = deparse(substitute(x)), arg = name,
-                          call = NULL) {
-  if (length(x) != 1) {
-    cli::cli_abort(c("'{name}' must be a scalar",
-                     i = "{name} has length {length(x)}"),
-                   call = call, arg = arg)
-  }
-}
-
-
-assert_character <- function(x, name = deparse(substitute(x)),
-                             arg = name, call = NULL) {
-  if (!is.character(x)) {
-    cli::cli_abort("'{name}' must be character", call = call, arg = arg)
-  }
-}
-
-
-assert_scalar_character <- function(x, name = deparse(substitute(x)),
-                                    arg = name, call = NULL) {
-  assert_scalar(x, name, arg = arg, call = call)
-  assert_character(x, name, arg = arg, call = call)
-}
diff --git a/inst/schema/report_list.json b/inst/schema/report_list.json
index 9b9bdbc..40d76bb 100644
--- a/inst/schema/report_list.json
+++ b/inst/schema/report_list.json
@@ -4,7 +4,8 @@
     "items": {
       "type": "object",
       "properties": {
-        "name": { "type": "string" }
+        "name": { "type": "string" },
+        "updated": { "type": "number" }
       }
     }
 }
diff --git a/tests/testthat/examples/data/orderly.R b/tests/testthat/examples/data/data.R
similarity index 100%
rename from tests/testthat/examples/data/orderly.R
rename to tests/testthat/examples/data/data.R
diff --git a/tests/testthat/helper-orderly-runner.R b/tests/testthat/helper-orderly-runner.R
index c2899d2..c3da15d 100644
--- a/tests/testthat/helper-orderly-runner.R
+++ b/tests/testthat/helper-orderly-runner.R
@@ -42,28 +42,3 @@ helper_add_git <- function(path) {
   gert::git_remote_add(url, repo = path)
   list(path = path, user = user, branch = branch, sha = sha, url = url)
 }
-
-
-initialise_git_repo <- function() {
-  t <- tempfile()
-  dir.create(t)
-  writeLines(c("# Example", "", "example repo"), file.path(t, "README.md"))
-  helper_add_git(t)
-}
-
-
-create_new_commit <- function(path, new_file = "new", message = "new message") {
-  writeLines("new file", file.path(path, new_file))
-  gert::git_add(".", repo = path)
-  user <- "author <author@example.com>"
-  gert::git_commit(message, author = user, committer = user, repo = path)
-}
-
-
-create_new_branch <- function(path, branch_name = "other") {
-  initial_branch <- gert::git_branch(repo = path)
-  gert::git_branch_create(branch_name, repo = path)
-  commit_sha <- create_new_commit(path, branch_name)
-  gert::git_branch_checkout(initial_branch, repo = path)
-  list(branch = branch_name, sha = commit_sha)
-}
diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index fcc69a6..f625c01 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -24,13 +24,13 @@ test_that("can list orderly reports", {
   path <- test_prepare_orderly_example(c("data", "parameters"))
   repo <- helper_add_git(path)
   endpoint <- orderly_runner_endpoint("GET", "/report/list", path)
-  get_reports_from_response <- function(res) {
-    vcapply(res$data, function(item) as.character(item[["name"]]))
-  }
 
   res <- endpoint$run(repo$branch)
   expect_equal(res$status_code, 200)
-  expect_setequal(get_reports_from_response(res), c("data", "parameters"))
+  expect_setequal(res$data$name, c("data", "parameters"))
+  # TODO: actually get modified time, looks like some issue with value
+  # coming back from gert::git_ls
+  expect_equal(res$data$update, c(0, 0))
 
   ## Delete a report on a 2nd branch
   gert::git_branch_create("other", repo = path)
@@ -42,11 +42,11 @@ test_that("can list orderly reports", {
   ## Can list items from this sha
   other_res <- endpoint$run(sha)
   expect_equal(other_res$status_code, 200)
-  expect_equal(get_reports_from_response(other_res), "parameters")
+  expect_equal(other_res$data$name, "parameters")
 
   ## We can still see all reports on main branch
   first_commit_res <- endpoint$run(repo$sha)
   expect_equal(first_commit_res$status_code, 200)
-  expect_setequal(get_reports_from_response(first_commit_res), 
+  expect_setequal(first_commit_res$data$name, 
                   c("data", "parameters"))
 })
diff --git a/tests/testthat/test-git.R b/tests/testthat/test-git.R
deleted file mode 100644
index eda36b3..0000000
--- a/tests/testthat/test-git.R
+++ /dev/null
@@ -1,48 +0,0 @@
-test_that("can do depth 1 clone", {
-  repo <- initialise_git_repo()
-  
-  first_commit <- repo$sha
-  second_commit <- create_new_commit(repo$path)
-  
-  first_clone <- git_clone_depth_1(repo$path, first_commit)
-  log <- gert::git_log(repo = first_clone)
-  expect_true(nrow(log) == 1)
-  expect_equal(log$commit, first_commit)
-  
-  second_clone <- git_clone_depth_1(repo$path, second_commit)
-  log <- gert::git_log(repo = second_clone)
-  expect_true(nrow(log) == 1)
-  expect_equal(log$commit, second_commit)
-})
-
-
-test_that("git ref to sha", {
-  testthat::skip_on_cran()
-  repo <- initialise_git_repo()
-  other <- create_new_branch(repo$path, "other")
-  sha1 <- git_ref_to_sha(repo$branch, repo$path)
-  sha2 <- git_ref_to_sha("other", repo$path)
-  
-  expect_match(sha1, "^[[:xdigit:]]{40}$")
-  expect_match(sha2, "^[[:xdigit:]]{40}$")
-  expect_true(sha1 != sha2)
-  
-  expect_equal(git_ref_to_sha("HEAD", repo$path), sha1)
-  expect_equal(git_ref_to_sha(substr(sha1, 1, 7), repo$path), sha1)
-  
-  expect_identical(git_ref_to_sha("unknown", repo$path),
-                   NA_character_)
-  expect_error(git_ref_to_sha("unknown", repo$path, TRUE),
-               "Git reference 'unknown' not found")
-})
-
-
-test_that("handle failure", {
-  testthat::skip_on_cran()
-  repo <- initialise_git_repo()
-  r <- git_run("unknown-command", repo = repo$path)
-  expect_false(r$success)
-  expect_error(
-    git_run("unknown-command", repo = repo$path, check = TRUE),
-    r$output, fixed = TRUE)
-})
diff --git a/tests/testthat/test-util-assert.R b/tests/testthat/test-util-assert.R
deleted file mode 100644
index 73d9105..0000000
--- a/tests/testthat/test-util-assert.R
+++ /dev/null
@@ -1,12 +0,0 @@
-test_that("assert_scalar", {
-  expect_error(assert_scalar(NULL), "must be a scalar")
-  expect_error(assert_scalar(numeric(0)), "must be a scalar")
-  expect_error(assert_scalar(1:2), "must be a scalar")
-})
-
-
-test_that("assert_character", {
-  expect_silent(assert_character("a"))
-  expect_error(assert_character(1), "must be character")
-  expect_error(assert_character(TRUE), "must be character")
-})

From caf41ca20015516097a2922e6d3bc402cc856057 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Fri, 23 Feb 2024 14:45:18 +0000
Subject: [PATCH 06/10] Add end to end test

---
 DESCRIPTION                   |  1 -
 tests/testthat/test-zzz-e2e.R | 22 ++++++++++++++++++----
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b726445..0f62af4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,7 +13,6 @@ Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "porcelain::porcel
 URL: https://github.com/mrc-ide/orderly.runner
 BugReports: https://github.com/mrc-ide/orderly.runner/issues
 Imports:
-    cli,
     docopt,
     gert,
     jsonlite,
diff --git a/tests/testthat/test-zzz-e2e.R b/tests/testthat/test-zzz-e2e.R
index 5df394e..7cc6ee9 100644
--- a/tests/testthat/test-zzz-e2e.R
+++ b/tests/testthat/test-zzz-e2e.R
@@ -1,8 +1,11 @@
+skip_if_not_installed("httr")
+root <- test_prepare_orderly_example(c("data", "parameters"))
+repo <- helper_add_git(root)
+bg <- porcelain::porcelain_background$new(api, list(root))
+bg$start()
+on.exit(bg$stop())
+
 test_that("can run server", {
-  skip_if_not_installed("httr")
-  root <- create_temporary_root(use_file_store = TRUE)
-  bg <- porcelain::porcelain_background$new(api, list(root))
-  bg$start()
   r <- bg$request("GET", "/")
   expect_equal(httr::status_code(r), 200)
 
@@ -14,3 +17,14 @@ test_that("can run server", {
   expect_equal(dat$data$orderly.runner,
                package_version_string("orderly.runner"))
 })
+
+test_that("can list reports", {
+  r <- bg$request("GET", "/report/list?hash=HEAD")
+  expect_equal(httr::status_code(r), 200)
+  
+  dat <- httr::content(r)
+  expect_equal(dat$status, "success")
+  expect_null(dat$errors)
+  reports <- vcapply(dat$data, "[[", "name")
+  expect_true(all(c("data", "parameters") %in% reports))
+})

From ac474f8d4e4a53b05c32f1fc73e099f26ae98c58 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Fri, 23 Feb 2024 17:24:39 +0000
Subject: [PATCH 07/10] Return the actual updated time

---
 R/api.R                      | 11 ++++++++---
 inst/schema/report_list.json |  2 +-
 tests/testthat/test-api.R    |  4 +---
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/R/api.R b/R/api.R
index 660c590..8825095 100644
--- a/R/api.R
+++ b/R/api.R
@@ -30,19 +30,24 @@ root <- function() {
   lapply(versions, scalar)
 }
 
+
 ##' @porcelain 
 ##'   GET /report/list => json(report_list)
 ##'   query hash :: string
 ##'   state root :: root
 report_list <- function(root, hash) {
   contents <- gert::git_ls(root, ref = hash)
+  ## Note there is a bug in current gert, and git_ls returns 0 for modified
+  ## and created time whenever called with a "ref". Get them via stat_files
+  ## for now
+  contents <- gert::git_stat_files(contents$path, ref = hash, repo = root)
   re <- "^src/([^/]+)/(\\1|orderly)\\.(yml|R)$"
   nms <- sub(re, "\\1", 
-             grep(re, contents$path, value = TRUE, perl = TRUE), 
+             grep(re, contents$file, value = TRUE, perl = TRUE), 
              perl = TRUE)
   last_changed <- function(nm) {
-    max(contents$modified[startsWith(contents$path, sprintf("src/%s", nm))])
+    max(contents$modified[startsWith(contents$file, sprintf("src/%s", nm))])
   }
   data.frame(name = nms, 
-             updated = vnapply(nms, last_changed, USE.NAMES = FALSE))
+             updated_time = vnapply(nms, last_changed, USE.NAMES = FALSE))
 }
diff --git a/inst/schema/report_list.json b/inst/schema/report_list.json
index 40d76bb..130b0de 100644
--- a/inst/schema/report_list.json
+++ b/inst/schema/report_list.json
@@ -5,7 +5,7 @@
       "type": "object",
       "properties": {
         "name": { "type": "string" },
-        "updated": { "type": "number" }
+        "updated_time": { "type": "number" }
       }
     }
 }
diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index f625c01..ecd24f5 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -28,9 +28,7 @@ test_that("can list orderly reports", {
   res <- endpoint$run(repo$branch)
   expect_equal(res$status_code, 200)
   expect_setequal(res$data$name, c("data", "parameters"))
-  # TODO: actually get modified time, looks like some issue with value
-  # coming back from gert::git_ls
-  expect_equal(res$data$update, c(0, 0))
+  expect_true(all(res$data$updated_time > (Sys.time() - 100)))
 
   ## Delete a report on a 2nd branch
   gert::git_branch_create("other", repo = path)

From bcdfd9db4a6e7cfb791e4d81bae40941c805fc73 Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Mon, 26 Feb 2024 17:06:37 +0000
Subject: [PATCH 08/10] Use development version of gert from GitHub

Current CRAN version contains an issue where if using git_ls()
with a ref then filesize, modified and created times are all set to 0.
This is fixed on GitHub
---
 DESCRIPTION | 3 ++-
 R/api.R     | 8 ++------
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0f62af4..4dbfe2c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,4 +28,5 @@ Suggests:
 Config/testthat/edition: 3
 Remotes:
     mrc-ide/orderly2,
-    reside-ic/porcelain
+    reside-ic/porcelain,
+    r-lib/gert
diff --git a/R/api.R b/R/api.R
index 8825095..5520ae5 100644
--- a/R/api.R
+++ b/R/api.R
@@ -37,16 +37,12 @@ root <- function() {
 ##'   state root :: root
 report_list <- function(root, hash) {
   contents <- gert::git_ls(root, ref = hash)
-  ## Note there is a bug in current gert, and git_ls returns 0 for modified
-  ## and created time whenever called with a "ref". Get them via stat_files
-  ## for now
-  contents <- gert::git_stat_files(contents$path, ref = hash, repo = root)
   re <- "^src/([^/]+)/(\\1|orderly)\\.(yml|R)$"
   nms <- sub(re, "\\1", 
-             grep(re, contents$file, value = TRUE, perl = TRUE), 
+             grep(re, contents$path, value = TRUE, perl = TRUE),
              perl = TRUE)
   last_changed <- function(nm) {
-    max(contents$modified[startsWith(contents$file, sprintf("src/%s", nm))])
+    max(contents$modified[startsWith(contents$path, sprintf("src/%s", nm))])
   }
   data.frame(name = nms, 
              updated_time = vnapply(nms, last_changed, USE.NAMES = FALSE))

From d2307d7a5fa5dcb297921fc4103da08bb538e56c Mon Sep 17 00:00:00 2001
From: Rob <39248272+r-ash@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:01:39 +0000
Subject: [PATCH 09/10] Update R/util.R

Co-authored-by: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
---
 R/util.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/util.R b/R/util.R
index 9919c03..1cc2dd9 100644
--- a/R/util.R
+++ b/R/util.R
@@ -13,8 +13,8 @@ package_version_string <- function(name) {
 }
 
 
-vcapply <- function(X, FUN, ...) { # nolint
-  vapply(X, FUN, character(1), ...)
+vcapply <- function(...) {
+  vapply(FUN.VALUE = character(1), ...)
 }
 
 

From 0808bb079e0b75ab06ccb80df2a04ab76cd43d3c Mon Sep 17 00:00:00 2001
From: Rob Ashton <r.ashton@imperial.ac.uk>
Date: Tue, 27 Feb 2024 15:16:07 +0000
Subject: [PATCH 10/10] Add minimum version number to gert

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4dbfe2c..c1e7bd1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,7 +14,7 @@ URL: https://github.com/mrc-ide/orderly.runner
 BugReports: https://github.com/mrc-ide/orderly.runner/issues
 Imports:
     docopt,
-    gert,
+    gert (>= 2.0.1),
     jsonlite,
     orderly2,
     porcelain,