Merge pull request #34 from vimc/vimc-4748

vimc · Jun 9, 2021 · 8e90453 · 8e90453
2 parents bfeb917 + c00636e
commit 8e90453
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^man-roxygen$
 ^appveyor\.yml$
 ^\.github$
+^\.lintr$
diff --git a/.lintr b/.lintr
@@ -0,0 +1,7 @@
+linters: with_defaults(
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    todo_comment_linter = NULL,
+    cyclocomp_linter = NULL
+    )
+exclusions: list("tests/testthat.R")
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
              person("Imperial College of Science, Technology and Medicine",
                     role = "cph"))
 Title: Vault Client for Secrets and Sensitive Data
-Version: 1.0.5
+Version: 1.1.0
 Description: Provides an interface to a 'HashiCorp' vault server over
   its http API (typically these are self-hosted; see
   <https://www.vaultproject.io>).  This allows for secure storage and
@@ -15,7 +15,7 @@ Description: Provides an interface to a 'HashiCorp' vault server over
   several backends including user name/password and authentication via
   'GitHub'.
 License: MIT + file LICENSE
-URL: https://github.com/vimc/vaultr, https://vimc.github.io/vaultr/
+URL: https://github.com/vimc/vaultr, https://www.vaccineimpact.org/vaultr/
 BugReports: https://github.com/vimc/vaultr/issues
 SystemRequirements: vault
 Imports:
@@ -30,7 +30,8 @@ Suggests:
     rmarkdown,
     testthat,
     withr
-RoxygenNote: 7.0.0
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 VignetteBuilder: knitr
 Language: en-GB
+Roxygen: list(markdown = TRUE)
diff --git a/R/aaa.R b/R/aaa.R
@@ -1,4 +1,19 @@
+##' Base object used by vaultr for all objects
+##'
+##' @title Base object type
+##'
+##' @name vault_client_object
+##'
 ##' @importFrom R6 R6Class
+##' @examples
+##'
+##' server <- vaultr::vault_test_server(if_disabled = message)
+##'
+##' if (!is.null(server)) {
+##'   client <- vaultr::vault_client(addr = server$addr)
+##'   client$operator$format()
+##'   client$operator$format(TRUE)
+##' }
 vault_client_object <- R6::R6Class(
   "vault_client_object",
   cloneable = FALSE,
@@ -10,16 +25,24 @@ vault_client_object <- R6::R6Class(
   ),
 
   public = list(
+    ##' @description Construct an object
+    ##'
+    ##' @param description Description for the object, will be printed
     initialize = function(description) {
       private$name <- sub("^(vault_|vault_client_)", "", class(self)[[1L]])
       private$help_name <- class(self)[[1L]]
       private$description <- description
     },
 
+    ##' @description Format method, overriding the R6 default
+    ##'
+    ##' @param brief Logical, indicating if this is the full format or
+    ##'   a brief (one line) format.
     format = function(brief = FALSE) {
       vault_client_format(self, brief, private$name, private$description)
     },
 
+    ##' @description Display help for this object
     help = function() {
       utils::help(private$help_name, package = "vaultr")
     }

diff --git a/R/server_manager.R b/R/server_manager.R
@@ -1,48 +1,47 @@
 ##' Control a server for use with testing.  This is designed to be
 ##' used only by other packages that wish to run tests against a vault
-##' server.  You will need to set \code{VAULTR_TEST_SERVER_BIN_PATH}
+##' server.  You will need to set `VAULTR_TEST_SERVER_BIN_PATH`
 ##' to point at the directory containing the vault binary.
 ##'
-##' Once created with \code{vault_test_server}, a server will stay
-##' alive for as long as the R process is alive \emph{or} until the
-##' \code{vault_server_instance} object goes out of scope and is
-##' garbage collected.  Calling \code{$kill()} will explicitly stop
+##' Once created with `vault_test_server`, a server will stay
+##' alive for as long as the R process is alive *or* until the
+##' `vault_server_instance` object goes out of scope and is
+##' garbage collected.  Calling `$kill()` will explicitly stop
 ##' the server, but this is not strictly needed.  See below for
 ##' methods to control the server instance.
 ##'
-##' The function \code{vault_test_server_install} will install a test
-##' server, but \emph{only} if the user sets the following environmental
+##' The function `vault_test_server_install` will install a test
+##' server, but *only* if the user sets the following environmental
 ##' variables:
-##' \itemize{
-##'   \item \code{VAULTR_TEST_SERVER_INSTALL} to \code{"true"} to opt in
-##' to the download.
-##'   \item \code{VAULTR_TEST_SERVER_BIN_PATH} to the directory where 
-##' the binary should be downloaded to.
-##'   \item \code{NOT_CRAN} to \code{"true"} to indicate this is not running
-##' on CRAN as it requires installation of a binary from a website.
-##' }
-##' This will download a ~100MB binary from \url{https://vaultproject.io}
-##' so use with care.  It is intended \emph{only} for use in automated
-##' testing environments.
 ##'
-##' @template vault_server_instance
+##' * `VAULTR_TEST_SERVER_INSTALL` to `"true"` to opt in to the
+##'   download.
+##'
+##' * `VAULTR_TEST_SERVER_BIN_PATH` to the directory where the binary
+##'   should be downloaded to.
+##'
+##' * `NOT_CRAN` to `"true"` to indicate this is not running on CRAN
+##'   as it requires installation of a binary from a website.
+##'
+##' This will download a ~100MB binary from https://vaultproject.io
+##' so use with care.  It is intended *only* for use in automated
+##' testing environments.
 ##'
 ##' @section Warning:
 ##'
-##' Starting a server in test mode must \emph{not} be used for
-##'   production under any circumstances.  As the name suggests,
-##'   \code{vault_test_server} is a server suitable for \emph{tests}
-##'   only and lacks any of the features required to make vault
-##'   secure.  Please see
-##'   \url{https://www.vaultproject.io/docs/concepts/dev-server.html}
+##' Starting a server in test mode must *not* be used for production
+##'   under any circumstances.  As the name suggests,
+##'   `vault_test_server` is a server suitable for *tests* only and
+##'   lacks any of the features required to make vault secure.  Please
+##'   see https://www.vaultproject.io/docs/concepts/dev-server.html
 ##'   for more information
 ##'
 ##' @section Warning:
 ##'
-##' The \code{vault_test_server_install} function will download a
+##' The `vault_test_server_install` function will download a
 ##'   binary from HashiCorp in order to use a vault server.  Use this
 ##'   function with care.  The download will happen from
-##'   \url{https://releases.hashicorp.com/vault} (over https).  This
+##'   https://releases.hashicorp.com/vault (over https).  This
 ##'   function is primarily designed to be used from continuous
 ##'   integration services only and for local use you are strongly
 ##'   recommended to curate your own installations.
@@ -51,24 +50,24 @@
 ##'
 ##' @param https Logical scalar, indicating if a https-using server
 ##'   should be created, rather than the default vault dev-mode
-##'   server.  This is still \emph{entirely} insecure, and uses self
+##'   server.  This is still *entirely* insecure, and uses self
 ##'   signed certificates that are bundled with the package.
 ##'
 ##' @param init Logical scalar, indicating if the https-using server
 ##'   should be initialised.
 ##'
 ##' @param if_disabled Callback function to run if the vault server is
 ##'   not enabled.  The default, designed to be used within tests, is
-##'   \code{testthat::skip}.  Alternatively, inspect the
-##'   \code{$enabled} property of the returned object.
+##'   `testthat::skip`.  Alternatively, inspect the
+##'   `$enabled` property of the returned object.
 ##'
 ##' @export
 ##' @rdname vault_test_server
 ##' @aliases vault_server_instance
 ##' @examples
 ##'
 ##' # Try and start a server; if one is not enabled (see details
-##' # above) then this will return \code{NULL}
+##' # above) then this will return NULL
 ##' server <- vault_test_server(if_disabled = message)
 ##'
 ##' if (!is.null(server)) {
@@ -85,7 +84,7 @@
 ##'
 ##'   # The server stops automatically when the server object is
 ##'   # garbage collected, or it can be turned off with the
-##'   # \code{kill} method:
+##'   # 'kill' method:
 ##'   server$kill()
 ##'   tryCatch(client$status(), error = function(e) message(e$message))
 ##' }
@@ -98,14 +97,18 @@ vault_test_server <- function(https = FALSE, init = TRUE,
 ##' @rdname vault_test_server
 ##'
 ##' @param quiet Suppress progress bars on install
-##' @param path Path in which to install vault test server. Leave as NULL to use the 
-##' \emph{VAULTR_TEST_SERVER_BIN_PATH} environment variable.
+##'
+##' @param path Path in which to install vault test server. Leave as
+##'   `NULL` to use the `VAULTR_TEST_SERVER_BIN_PATH` environment
+##'   variable.
+##'
 ##' @param version Version of vault to install
-##' @param platform For testing, overwrite the platform vault is being installed
-##' on, with either "windows", "darwin" or "linux".
+##'
+##' @param platform For testing, overwrite the platform vault is being
+##'   installed on, with either "windows", "darwin" or "linux".
 ##'
 ##' @export
-vault_test_server_install <- function(path = NULL, quiet = FALSE, 
+vault_test_server_install <- function(path = NULL, quiet = FALSE,
                                       version = "1.0.0",
                                       platform = vault_platform()) {
   if (!identical(Sys.getenv("NOT_CRAN"), "true")) {
@@ -120,7 +123,7 @@ vault_test_server_install <- function(path = NULL, quiet = FALSE,
       stop("VAULTR_TEST_SERVER_BIN_PATH is not set")
     }
   }
-  
+
   dir_create(path)
   dest <- file.path(path, vault_exe_filename(platform))
   if (file.exists(dest)) {
@@ -269,8 +272,6 @@ vault_server_start_dev <- function(bin, port) {
     Sys.sleep(0.5) # nocov
   }
 
-  txt2 <- readLines(process$get_error_file())
-
   ## See https://www.vaultproject.io/docs/secrets/kv/kv-v2.html#setup
   ##
   ## > when running a dev-mode server, the v2 kv secrets engine is
@@ -350,7 +351,7 @@ vault_url <- function(version, platform = vault_platform(), arch = "amd64") {
 }
 
 vault_exe_filename <- function(platform = vault_platform()) {
-  if (platform == 'windows') {
+  if (platform == "windows") {
     "vault.exe"
   } else {
     "vault"

diff --git a/R/util.R b/R/util.R
@@ -9,11 +9,11 @@ to_json <- function(x) {
 }
 
 
-`%||%` <- function(a, b) {
+`%||%` <- function(a, b) { # nolint
   if (is.null(a)) b else a
 }
 
-`%&&%` <- function(a, b) {
+`%&&%` <- function(a, b) { # nolint
   if (is.null(a)) NULL else b
 }
 
@@ -31,10 +31,11 @@ is_absolute_path <- function(path) {
   substr(path, 1, 1) == "/"
 }
 
-vlapply <- function(X, FUN, ...) {
+vlapply <- function(X, FUN, ...) { # nolint
   vapply(X, FUN, logical(1), ...)
 }
-vcapply <- function(X, FUN, ...) {
+
+vcapply <- function(X, FUN, ...) { # nolint
   vapply(X, FUN, character(1), ...)
 }
 
@@ -53,7 +54,7 @@ strsub <- function(str, tr) {
   str
 }
 
-Sys_getenv <- function(name, unset = NULL, mode = "character") {
+Sys_getenv <- function(name, unset = NULL, mode = "character") { # nolint
   value <- Sys.getenv(name, NA_character_)
   if (is.na(value)) {
     value <- unset
@@ -171,7 +172,7 @@ decode64 <- function(input) {
 }
 
 
-isFALSE <- function(x) {
+isFALSE <- function(x) { # nolint
   is.logical(x) && length(x) == 1L && !is.na(x) && !x
 }