Merge pull request #39 from getwilds/dev

Regulated data features

Author: sckott

.github/workflows/lint.yaml

@@ -1,9 +1,6 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 on:
   push:
-    branches: [main, auth-change]
   pull_request:
-    branches: [main, auth-change]
 
 name: lint
 
@@ -15,17 +12,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - name: Install Air
+        uses: posit-dev/setup-air@v1
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::lintr, local::.
-          needs: lint
-
-      - name: Lint
-        run: lintr::lint_package()
-        shell: Rscript {0}
-        env:
-          LINTR_ERROR_ON_LINT: true
+      - name: Check
+        run: air format . --check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: proofr
 Title: Client for the PROOF API
-Version: 0.4.0
-Authors@R: 
+Version: 0.5.0
+Authors@R:
     person("Scott", "Chamberlain", , "sachamber@fredhutch.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1444-9135"))
 Description: Client for the PROOF API.
@@ -15,12 +15,12 @@ Imports:
     cli,
     glue,
     httr2
-Suggests: 
+Suggests:
     jsonlite,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
-    webmockr (>= 1.0.0),
+    webmockr (>= 2.2.0),
     withr
 Config/testthat/edition: 3
 VignetteBuilder: knitr

Makefile

@@ -31,12 +31,7 @@ readme:
 	${RSCRIPT} -e "knitr::knit('README.Rmd')"
 
 lint_package:
-	${RSCRIPT} -e "lintr::lint_package()"
+	air format . --check
 
-# use: `make style_file FILE=stuff.R`
-# ("R/" is prepended); accepts 1 file only
-style_file:
-	${RSCRIPT} -e 'styler::style_file(${FILE_TARGET})'
-
-style_package:
-	${RSCRIPT} -e "styler::style_pkg()"
+fix_package:
+	air format .

NEWS.md

@@ -1,3 +1,8 @@
+# proofr v0.5.0
+
+* Support for regulated data features in the PROOF API
+* Formatting code - changed to using Posit's air formatter
+
 # proofr v0.4.0
 
 * Bumping timeout from 5 seconds to 20 seconds (@sckott in [direct commit](https://github.com/getwilds/proofr/commit/cbe9062fd73e61992b46035e7ac2241cd8de2541))

R/start.R

@@ -10,6 +10,8 @@
 #' 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
+#' @param regulated_data (logical) whether to use a scratch directory
+#' in regulated storage.
 #' @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
@@ -21,11 +23,18 @@
 #' You do however need to have a Cromwell server up and running to
 #' retrieve data.
 #' @return A list with fields:
-#' - `job_id` (character) - the job ID
+#' - `job_id` (character) - the job ID =
 #' - `info` (character) - message
-proof_start <- function(slurm_account = NULL, token = NULL) {
+proof_start <- function(
+  slurm_account = NULL,
+  token = NULL,
+  regulated_data = FALSE
+) {
   request(make_url("cromwell-server")) |>
-    req_body_json(list(slurm_account = slurm_account)) |>
+    req_body_json(list(
+      slurm_account = slurm_account,
+      regulated_data = regulated_data
+    )) |>
     proof_header(token) |>
     req_timeout(proofr_env$timeout_sec) |>
     req_error(body = error_body) |>

R/utils.R

@@ -9,7 +9,9 @@ make_url <- function(...) {
 assert <- function(x, y) {
   if (!is.null(x)) {
     if (!inherits(x, y)) {
-      stop(deparse(substitute(x)), " must be of class ",
+      stop(
+        deparse(substitute(x)),
+        " must be of class ",
         paste0(y, collapse = ", "),
         call. = FALSE
       )

man/proof_start.Rd

@@ -44,7 +44,6 @@ test_that("proof_start - success", {
   expect_type(auth_res, "character")
   expect_equal(auth_res, "somerandomstring")
 
-
   stub_registry_clear()
   disable(quiet = TRUE)
   Sys.unsetenv("PROOF_TOKEN")

tests/testthat/test-proof_authenticate.R

@@ -17,7 +17,6 @@ test_that("proof_cancel - success", {
   expect_type(cancel_res$message, "character")
   expect_match(cancel_res$message, "cancelled")
 
-
   stub_registry_clear()
   disable(quiet = TRUE)
 })
@@ -37,7 +36,6 @@ test_that("proof_cancel - not running, can not cancel", {
     expect_error(proof_cancel(), "Additional context")
   })
 
-
   stub_registry_clear()
   disable(quiet = TRUE)
 })

tests/testthat/test-proof_cancel.R

@@ -2,7 +2,9 @@
 
 test_that("proof_header", {
   # errors if no env var set and no string supplied
-  expect_error(proof_header(request("")), "token not found")
+  withr::with_envvar(new = c("PROOF_TOKEN" = ""), {
+    expect_error(proof_header(request("")), "token not found")
+  })
 
   # returns token if given
   expect_match(proof_header(request(""), "adf")$headers[[1]], "adf")