fix: Keep auditing when the sys-deps check can't run (0.8.11)

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: audit.connect
 Title: Posit Connect Health Check
-Version: 0.8.10
+Version: 0.8.11
 Authors@R:
     person("Jumping", "Rivers", , "info@jumpingrivers.com", role = c("aut", "cre"))
 Description: Posit Connect Health Check. Deploys various content types to
@@ -10,7 +10,7 @@ License: file LICENSE
 Depends:
     R (>= 4.1.0)
 Imports:
-    audit.base (>= 0.7.2),
+    audit.base (>= 0.7.6),
     cli,
     connectapi (>= 0.12.1),
     dplyr,

NEWS.md

@@ -1,3 +1,10 @@
+# audit.connect 0.8.11
+
+## Bug fixes and minor improvements
+
+* `check()` carries on when the system-library check can't run. An error from the endpoint, an unexpected reply or an unsupported OS gives a warning and `sys_deps = NA`, and the deployment checks still run (#63).
+* The sys-deps endpoint lists installed packages on Debian, Rocky Linux and AlmaLinux, as well as Ubuntu and RHEL. Requires audit.base 0.7.6 (#63).
+
 # audit.connect 0.8.10
 
 ## Bug fixes and minor improvements

R/check_sys_deps.R

@@ -39,13 +39,33 @@ check_sys_deps = function(debug_level = 0:2) {
   # Ping endpoint
   url = paste0(get_deploy_url(content), "installed")
   auth_key = paste0("Key ", get_token())
-  resp = httr::GET(url, httr::add_headers(Authorization = auth_key))
-  rtn = jsonlite::parse_json(rawToChar(resp$content))
-  # Read by check_connect_timezone(), as the endpoint is the only code that runs on Connect
-  .connect$timezone = unlist(rtn$timezone)
-
-  clean_libs = audit.base::clean_libs(rtn$os_release, rtn$libs)
-  audit.base::check_sys_deps(rtn$os_release, clean_libs, debug_level)
+  resp = httr::GET(url, httr::add_headers(Authorization = auth_key), httr::timeout(120))
+  if (httr::http_error(resp)) {
+    cli::cli_warn(
+      "Can't check system libraries: the endpoint returned {httr::http_status(resp)$message}"
+    )
+    return(NA)
+  }
+  # An unsupported OS or an unexpected reply warns, so the deployment checks still run
+  tryCatch(
+    {
+      rtn = jsonlite::parse_json(rawToChar(resp$content))
+      # Read by check_connect_timezone(), as the endpoint is the only code that runs on Connect
+      .connect$timezone = unlist(rtn$timezone)
+      os_release = unlist(rtn$os_release)
+      libs = unlist(rtn$libs)
+      clean_libs = audit.base::clean_libs(os_release, libs)
+      # clean_libs() has warned that it can't read the package list
+      if (anyNA(clean_libs)) {
+        return(NA)
+      }
+      audit.base::check_sys_deps(os_release, clean_libs, debug_level)
+    },
+    error = function(e) {
+      cli::cli_warn(c("Can't check system libraries", "x" = conditionMessage(e)))
+      NA
+    }
+  )
 }
 
 setup_plumber_sys_deps_endpoint = function(app_dir, debug_level) {

inst/extdata/check_sys_deps/manifest.json

@@ -674,7 +674,7 @@
       "checksum": "9fcd95b1ccc5ca6dba0ad125b62c3747"
     },
     "plumber.R": {
-      "checksum": "ed571a06f3580f5202a258fb5e8d6bb5"
+      "checksum": "cb29cfd98c2279f36771c28f0619831e"
     },
     "renv.lock": {
       "checksum": "a564e763ab0a9b503272f0c962cef9c6"

inst/extdata/check_sys_deps/plumber.R

@@ -3,17 +3,35 @@
 #
 # Commented out. Don't need plumber to deploy
 library("plumber")
+
+# apt or yum, from os-release ID and ID_LIKE, so Debian, Rocky and AlmaLinux are listed too.
+# audit.base decides whether Posit Package Manager supports the OS.
+package_tool = function(os_release) {
+  ids = sub("^ID(_LIKE)?=", "", os_release[grepl("^ID(_LIKE)?=", os_release)])
+  ids = strsplit(tolower(gsub("\"", "", ids)), " ")
+  ids = unlist(ids)
+  if (any(ids %in% c("debian", "ubuntu"))) {
+    "apt"
+  } else if (any(ids %in% c("rhel", "centos", "fedora"))) {
+    "yum"
+  } else {
+    NA_character_
+  }
+}
+
 #* @apiTitle Installed Sys Deps
 #* @apiDescription Returns the OS, installed libraries and timezone of the connect server
 #* @get /installed
 function() {
   os_release = readLines("/etc/os-release")
-  if (any(grepl("[u|U]buntu", os_release))) {
+  tool = package_tool(os_release)
+  if (identical(tool, "apt")) {
     libs = system2("apt", args = c("list", "--installed"), stdout = TRUE)
-  } else if (any(grepl("red hat|centos", os_release, ignore.case = TRUE))) {
+  } else if (identical(tool, "yum")) {
     libs = system2("yum", args = c("list", "installed"), stdout = TRUE)
   } else {
-    os_release = libs = NA
+    # Still send os_release, so audit.base can say which OS isn't supported
+    libs = NA
   }
 
   # Sys.timezone() warns when timedatectl fails, but can still find the timezone.

tests/testthat/test-cleanup.R

@@ -72,3 +72,33 @@ test_that("cleanup_quarto() deletes by title when the deploy left no record", {
   expect_identical(calls$deleted, "a")
   expect_false(dir.exists(tmp_dir))
 })
+
+test_that("A bad endpoint reply or unsupported OS warns instead of stopping check()", {
+  testthat::local_mocked_bindings(
+    get_server = function(...) "https://connect.example.com/",
+    get_token = function(...) "key",
+    get_deploy_url = function(...) "https://connect.example.com/content/1/",
+    cleanup_plumber = function(...) NULL,
+    setup_plumber_sys_deps_endpoint = function(...) structure(list(), class = "Content")
+  )
+  testthat::local_mocked_bindings(poll_task = function(x, ...) x, .package = "connectapi")
+  reply = function(status, body) {
+    structure(
+      list(status_code = status, content = charToRaw(body), headers = list()),
+      class = "response"
+    )
+  }
+  replies = list(
+    reply(500L, "Internal Server Error"),
+    reply(200L, "<html>not JSON</html>"),
+    reply(
+      200L,
+      '{"os_release":["PRETTY_NAME=\\"Arch Linux\\"","ID=arch"],"libs":[null],"timezone":[""]}'
+    )
+  )
+  for (resp in replies) {
+    testthat::local_mocked_bindings(GET = function(...) resp, .package = "httr")
+    expect_warning(sys_deps <- check_sys_deps(debug_level = 0), "system libraries") # nolint
+    expect_identical(sys_deps, NA)
+  }
+})

tests/testthat/test-timezone.R

@@ -1,3 +1,15 @@
+# The endpoint and its helper, without library("plumber")
+load_sys_deps_endpoint = function() {
+  plumber_file = system.file("extdata", "check_sys_deps", "plumber.R", package = "audit.connect")
+  exprs = parse(plumber_file)
+  env = new.env()
+  for (expr in exprs[-c(1L, length(exprs))]) {
+    eval(expr, env)
+  }
+  env$endpoint = eval(exprs[[length(exprs)]], env)
+  env
+}
+
 test_that("check_connect_timezone() reports set, unset and unknown", {
   on.exit(assign("timezone", NULL, envir = .connect))
   .connect$timezone = "Europe/London"
@@ -11,14 +23,27 @@ test_that("check_connect_timezone() reports set, unset and unknown", {
 test_that("The sys deps endpoint returns a timezone that survives JSON", {
   # Connect only runs on Linux, so the endpoint does too
   skip_if_not(Sys.info()[["sysname"]] == "Linux")
-  plumber_file = system.file("extdata", "check_sys_deps", "plumber.R", package = "audit.connect")
-  exprs = parse(plumber_file)
-  endpoint = eval(exprs[[length(exprs)]])
-  rtn = endpoint()
+  env = load_sys_deps_endpoint()
+  rtn = env$endpoint()
   expect_type(rtn$timezone, "character")
   expect_length(rtn$timezone, 1)
   for (auto_unbox in c(TRUE, FALSE)) {
     json = jsonlite::toJSON(rtn["timezone"], auto_unbox = auto_unbox)
     expect_identical(unlist(jsonlite::parse_json(json)$timezone), rtn$timezone)
   }
 })
+
+test_that("The sys deps endpoint lists packages on Debian and RHEL rebuilds", {
+  env = load_sys_deps_endpoint()
+  os_releases = list(
+    apt = c("ID=ubuntu", "ID_LIKE=debian"),
+    apt = "ID=debian",
+    yum = c("ID=\"rocky\"", "ID_LIKE=\"rhel centos fedora\""),
+    yum = c("ID=\"almalinux\"", "ID_LIKE=\"rhel centos fedora\""),
+    yum = c("ID=\"rhel\"", "ID_LIKE=\"fedora\"")
+  )
+  for (i in seq_along(os_releases)) {
+    expect_identical(env$package_tool(os_releases[[i]]), names(os_releases)[i])
+  }
+  expect_identical(env$package_tool(c("ID=\"opensuse-leap\"", "ID_LIKE=\"suse\"")), NA_character_)
+})