Merge pull request #31 from getwilds/dev

proofr v0.3.0 Updates

DESCRIPTION

@@ -1,26 +1,26 @@
 Package: proofr
 Title: Client for the PROOF API
-Version: 0.2.0.94
+Version: 0.2.1.91
 Authors@R: 
     person("Scott", "Chamberlain", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1444-9135"))
 Description: Client for the PROOF API.
-URL: http://getwilds.org/proofr/ (website)
-    https://github.com/getwilds/proofr (devel)
+URL: http://getwilds.org/proofr/, https://github.com/getwilds/proofr
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
+Depends: R (>= 4.1.0)
 Imports:
     cli,
     glue,
-    httr
+    httr2
 Suggests: 
     jsonlite,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
-    webmockr,
+    webmockr (>= 1.0.0),
     withr
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -3,18 +3,18 @@
 export(proof_authenticate)
 export(proof_cancel)
 export(proof_header)
+export(proof_info)
 export(proof_start)
 export(proof_status)
 export(proof_timeout)
 importFrom(cli,cli_progress_bar)
 importFrom(cli,cli_progress_update)
-importFrom(httr,DELETE)
-importFrom(httr,GET)
-importFrom(httr,POST)
-importFrom(httr,add_headers)
-importFrom(httr,content)
-importFrom(httr,http_error)
-importFrom(httr,http_status)
-importFrom(httr,status_code)
-importFrom(httr,stop_for_status)
-importFrom(httr,timeout)
+importFrom(httr2,req_body_json)
+importFrom(httr2,req_error)
+importFrom(httr2,req_headers)
+importFrom(httr2,req_method)
+importFrom(httr2,req_perform)
+importFrom(httr2,req_timeout)
+importFrom(httr2,request)
+importFrom(httr2,resp_body_json)
+importFrom(httr2,resp_status)

R/auth.R

@@ -12,11 +12,12 @@ find_token <- function(token = NULL) {
 #' Get header for PROOF API calls
 #'
 #' @export
+#' @param req An `httr2` request. required
 #' @param token (character) PROOF API token. optional
-#' @return A `request` S3 class with the HTTP header that can be passed
-#' to `httr::GET()`, `httr::POST()`, etc.
-proof_header <- function(token = NULL) {
-  add_headers(Authorization = paste0("Bearer ", find_token(token)))
+#' @return An `httr2_request` S3 class adding an HTTP header for
+#' `Authorization` with the value in `token`
+proof_header <- function(req, token = NULL) {
+  req_headers(req, Authorization = paste0("Bearer ", find_token(token)))
 }
 
 #' Authenticate with PROOF API
@@ -27,20 +28,21 @@ proof_header <- function(token = NULL) {
 #' @inheritSection proof_status Timeout
 #' @return A single token (character) for bearer authentication with
 #' the PROOF API
+#' @details We strongly recommend to not supply `password` as plain text like
+#' `proof_authenticate(username = "jane", password = "mypassword")`, but rather
+#' pull in your password from an environment variable stored outside of R like
+#' `proof_authenticate(username = "jane", password = Sys.getenv("HUTCH_PWD"))`
 proof_authenticate <- function(username, password) {
   assert(username, "character")
   assert(password, "character")
 
-  response <- POST(make_url("authenticate"),
-    body = list(
+  response <- request(make_url("authenticate")) |>
+    req_body_json(list(
       username = username,
       password = password
-    ),
-    encode = "json",
-    timeout(proofr_env$timeout_sec)
-  )
-  stop_for_status(response)
-  parsed <- content(response, as = "parsed")
-  token <- parsed$token
-  token
+    )) |>
+    req_timeout(proofr_env$timeout_sec) |>
+    req_perform() |>
+    resp_body_json()
+  response$token
 }

R/cancel.R

@@ -2,18 +2,17 @@
 #'
 #' @export
 #' @inheritParams proof_start
-#' @references <https://github.com/FredHutch/proof-api#delete-cromwell-server>
 #' @inheritSection proof_status Timeout
 #' @return On success, a list with a single field:
 #' - `message` (character)
 #'
 #' If run when there's no Cromwell server running, an HTTP error
 proof_cancel <- function(token = NULL) {
-  response <- DELETE(
-    make_url("cromwell-server"),
-    proof_header(token),
-    timeout(proofr_env$timeout_sec)
-  )
-  stop_for_message(response)
-  content(response, as = "parsed")
+  request(make_url("cromwell-server")) |>
+    req_method("DELETE") |>
+    proof_header(token) |>
+    req_timeout(proofr_env$timeout_sec) |>
+    req_error(body = error_body) |>
+    req_perform() |>
+    resp_body_json()
 }

R/http.R

@@ -1,13 +1,6 @@
-stop_for_message <- function(response) {
-  if (http_error(response)) {
-    parsed <- tryCatch(content(response), error = function(e) e)
-    if (inherits(parsed, "error")) stop_for_status(response)
-    if (!is.list(parsed)) stop_for_status(response)
-    msg <- glue::glue(
-      "{http_status(response)$reason}",
-      " (HTTP {status_code(response)})",
-      " {parsed$message}"
-    )
-    stop(msg, call. = FALSE)
-  }
+error_body <- function(response) {
+  parsed <- resp_body_json(response)
+  glue::glue(
+    "Additional context: {parsed$message}"
+  )
 }

R/info.R

@@ -0,0 +1,16 @@
+#' Get information about PROOF server
+#'
+#' @export
+#' @return A list with fields:
+#' - `branch` (character): git branch of API
+#' - `commit_sha` (character): SHA of the git commit of the API
+#' - `short_commit_sha` (character): the first eight characters of `commit_sha`
+#' - `commit_message` (character): commit message of API's most recent commit
+#' - `tag` (character): tag of most recent commit/release version
+proof_info <- function() {
+  request(make_url("info")) |>
+    req_timeout(proofr_env$timeout_sec) |>
+    req_error(body = error_body) |>
+    req_perform() |>
+    resp_body_json()
+}

R/proofr-package.R

@@ -1,9 +1,14 @@
 #' @keywords internal
+#' @section Base URL for PROOF API:
+#' The base URL for the PROOF API can be changed by setting the environment
+#' variable `PROOF_API_BASE_URL`. It can be set for an R session or for
+#' function by function use as we check that env var in each function call
+#' to the API
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom httr GET POST DELETE add_headers content
-#' stop_for_status timeout http_status status_code
-#' http_error
+#' @importFrom httr2 request req_perform req_headers
+#' req_timeout req_body_json req_method req_error
+#' resp_status resp_body_json
 ## usethis namespace: end
 NULL

R/start.R

@@ -10,11 +10,9 @@
 #' here as a string. Either pass it using [Sys.getenv()] or save your
 #' token as an env var and then passing nothing to this param and we'll find
 #' it
-#' @references <https://github.com/FredHutch/proof-api/#post-cromwell-server>
 #' @details Does not return PROOF/Cromwell server URL, for that you have to
 #' periodically call [proof_status()], or wait for the email from the
-#' PROOF API. See the link to proof-api for more details about the
-#' slurm account.
+#' PROOF API
 #' @inheritSection proof_status Timeout
 #' @section Cromwell Server uptime:
 #' The Cromwell server started by this function will run for 7 days
@@ -26,13 +24,11 @@
 #' - `job_id` (character) - the job ID
 #' - `info` (character) - message
 proof_start <- function(slurm_account = NULL, token = NULL) {
-  response <- POST(
-    make_url("cromwell-server"),
-    proof_header(token),
-    body = list(slurm_account = slurm_account),
-    encode = "json",
-    timeout(proofr_env$timeout_sec)
-  )
-  stop_for_message(response)
-  content(response, as = "parsed")
+  request(make_url("cromwell-server")) |>
+    req_body_json(list(slurm_account = slurm_account)) |>
+    proof_header(token) |>
+    req_timeout(proofr_env$timeout_sec) |>
+    req_error(body = error_body) |>
+    req_perform() |>
+    resp_body_json()
 }

R/status.R

@@ -6,7 +6,6 @@
 #' @param wait (logical) if `TRUE` wait for the server to be ready to
 #' interact with. if `FALSE` return immediately, then you'll want to call
 #' this function again until you get the server URL
-#' @references <https://github.com/FredHutch/proof-api#get-cromwell-server>
 #' @section Timeout:
 #' If the PROOF API is unavailable, this function will timeout after
 #' 5 seconds. Contact the package maintainer if you get a timeout error.
@@ -25,13 +24,12 @@ proof_status <- function(wait = FALSE, token = NULL) {
 }
 
 fetch_status <- function(token = NULL) {
-  response <- GET(
-    make_url("cromwell-server"),
-    proof_header(token),
-    timeout(proofr_env$timeout_sec)
-  )
-  stop_for_message(response)
-  content(response, as = "parsed")
+  request(make_url("cromwell-server")) |>
+    proof_header(token) |>
+    req_timeout(proofr_env$timeout_sec) |>
+    req_error(body = error_body) |>
+    req_perform() |>
+    resp_body_json()
 }
 
 fetch_wait <- function(token) {

R/timeout.R

@@ -2,10 +2,10 @@
 #'
 #' @export
 #' @param sec (integer/numeric) number of seconds after which
-#' requests will timeout. default: 5 sec (5000 ms)
+#' requests will timeout. default: 10 sec (10000 ms)
 #' @references <https://httr.r-lib.org/reference/timeout.html>
 #' @return nothing, side effect of setting the timeout for requests
-proof_timeout <- function(sec = 5) {
+proof_timeout <- function(sec = 10) {
   assert(sec, c("integer", "numeric"))
   proofr_env$timeout_sec <- sec
 }

R/utils.R

@@ -1,7 +1,8 @@
-
 make_url <- function(...) {
-  proof_base <- Sys.getenv("PROOF_API_BASE_URL",
-                           "https://proof-api.fredhutch.org")
+  proof_base <- Sys.getenv(
+    "PROOF_API_BASE_URL",
+    "https://proof-api.fredhutch.org"
+  )
   file.path(proof_base, ...)
 }
 

README.Rmd

@@ -41,6 +41,7 @@ To get started with `proofr`, see the [Getting Started vignette](https://getwild
 ## Notes
 
 - There are no plans to submit this package to CRAN. Therefore, you should not depend on this package in any packages you have on CRAN.
+- Base URL: The base URL for the PROOF API can be changed by setting the environment variable `PROOF_API_BASE_URL`. It can be set for an R session or for function by function use as we check that env var in each function call to the API.
 
 ## Bugs? Features?
 

README.md

@@ -33,6 +33,7 @@ To get started with `proofr`, see the [Getting Started vignette](https://getwild
 ## Notes
 
 - There are no plans to submit this package to CRAN. Therefore, you should not depend on this package in any packages you have on CRAN.
+- Base URL: The base URL for the PROOF API can be changed by setting the environment variable `PROOF_API_BASE_URL`. It can be set for an R session or for function by function use as we check that env var in each function call to the API.
 
 ## Bugs? Features?