merge from main

DESCRIPTION

@@ -1,15 +1,14 @@
 Package: rcromwell
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 3.2.4.91
+Version: 3.2.6.9100
 Authors@R: c(
     person("Amy", "Paguirigan", role = "aut",
            comment = c(ORCID = "0000-0002-6819-9736")),
     person("Scott", "Chamberlain", , "sachamber@fredhutch.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1444-9135")),
     person("Fred Hutchinson Cancer Center", , , "wilds@fredhutch.org", role = "fnd")
   )
-URL: http://getwilds.org/rcromwell/ (website)
-    https://github.com/getwilds/rcromwell (devel)
+URL: https://getwilds.org/rcromwell, https://github.com/getwilds/rcromwell
 BugReports: https://github.com/getwilds/rcromwell/issues
 Description: A repo containing a basic R package for using Cromwell with WDL workflows via R.
 Imports:
@@ -33,11 +32,8 @@ Suggests:
     rmarkdown,
     roxyglobals,
     testthat (>= 3.0.0),
-    vcr (>= 0.6.0),
-    webmockr
-Remotes:
-    ropensci/vcr@httr2,
-    ropensci/webmockr@httr2
+    vcr (>= 1.6.0),
+    webmockr (>= 1.0.0)
 Config/testthat/edition: 3
 Config/roxyglobals/filename: globals.R
 Config/roxyglobals/unique: FALSE

NAMESPACE

@@ -21,7 +21,9 @@ export(workflow_inputs)
 export(workflow_options)
 importFrom(curl,form_file)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,any_of)
 importFrom(dplyr,as_tibble)
+importFrom(dplyr,relocate)
 importFrom(dplyr,tibble)
 importFrom(glue,glue)
 importFrom(httr2,req_body_multipart)

NEWS.md

@@ -1,3 +1,11 @@
+# rcromwell 3.2.5
+
+* gains new function `cromwell_labels` that hits the `/labels` route (#43) (#45)
+* remove comment about failures not working (#35)
+* add prior art section to readme with one entry (#30)
+* reorder output columns of `cromwell_workflow` and always return tibble for `cromwell_call` (#42) (#46)
+* better links in readme to docs (#41)
+
 # rcromwell 3.2.1
 
 * fix `cromwell_submit_batch` - internally changed `workflow_options` to `workflowOptions` (#32)

R/cromwellCall.R

@@ -252,6 +252,6 @@ cromwell_call <- function(workflow_id, url = cw_url(), token = NULL) {
     # with Shiny apps easier
     just_calls <- dplyr::tibble("workflow_id" = "No call metadata available.")
   }
-  return(just_calls)
+  return(dplyr::as_tibble(just_calls))
 }
 # nolint end

R/cromwellJobs.R

@@ -106,5 +106,12 @@ cromwell_jobs_process <- function(jobs_data) {
   } else {
     cr_table <- dplyr::tibble("workflow_id" = NA)
   }
+
+  # specific column order if columns exist (via `any_of`)
+  columns_order <- c(
+    "workflow_name", "workflow_id", "status", "submission", "start",
+    "end", "workflowDuration"
+  )
+  cr_table <- dplyr::relocate(cr_table, any_of(columns_order))
   return(cr_table)
 }

R/cromwellSubmitBatch.R

@@ -66,8 +66,12 @@ cromwell_submit_batch_query <- function(
     )
   }
   if (!is.null(labels)) {
+    labels_temp_file <- tempfile(pattern = "rcromwell_", fileext = ".json")
+    cat(jsonlite::toJSON(as.list(labels), auto_unbox = TRUE),
+      file = labels_temp_file
+    )
     body <- c(body,
-      labels = list(jsonlite::toJSON(as.list(labels), auto_unbox = TRUE))
+      labels = lst_upload_file(labels_temp_file)
     )
   }
   body

R/rcromwell-package.R

@@ -4,7 +4,7 @@
 ## usethis namespace: start
 #' @importFrom glue glue
 #' @importFrom rlang abort
-#' @importFrom dplyr as_tibble tibble %>%
+#' @importFrom dplyr as_tibble tibble relocate any_of %>%
 #' @importFrom lubridate now with_tz ymd_hms
 #' @importFrom purrr discard flatten keep map map_dfr pluck reduce
 #' @importFrom httr2 request req_headers req_perform req_error

README.Rmd

@@ -35,7 +35,7 @@ pak::pak("getwilds/rcromwell")
 
 ## Documentation
 
-Go to <http://getwilds.org/rcromwell/> for `rcromwell` package documentation. Go to the **Get Started** vignette to get started!
+Go to <http://getwilds.org/rcromwell/> for `rcromwell` package documentation. Go to the [Get Started vignette](https://getwilds.org/rcromwell/articles/rcromwell.html) to get started, or [reference page](https://getwilds.org/rcromwell/reference/index.html) for the function documentation.
 
 ## Bugs? Features?
 
@@ -48,3 +48,7 @@ Please note that the rcromwell project is released with a [Contributor Code of C
 ## License
 
 [MIT](LICENSE.md)
+
+## Prior art
+
+- [wdlRunR](https://github.com/seandavi/wdlRunR) - archived package/repo

README.md

@@ -27,7 +27,7 @@ pak::pak("getwilds/rcromwell")
 
 ## Documentation
 
-Go to <http://getwilds.org/rcromwell/> for `rcromwell` package documentation. Go to the **Get Started** vignette to get started!
+Go to <http://getwilds.org/rcromwell/> for `rcromwell` package documentation. Go to the [Get Started vignette](https://getwilds.org/rcromwell/articles/rcromwell.html) to get started, or [reference page](https://getwilds.org/rcromwell/reference/index.html) for the function documentation.
 
 ## Bugs? Features?
 
@@ -40,3 +40,7 @@ Please note that the rcromwell project is released with a [Contributor Code of C
 ## License
 
 [MIT](LICENSE.md)
+
+## Prior art
+
+- [wdlRunR](https://github.com/seandavi/wdlRunR) - archived package/repo

_pkgdown.yml

@@ -27,6 +27,7 @@ reference:
       - cromwell_failures
       - cromwell_glob
       - cromwell_jobs
+      - cromwell_labels
       - cromwell_logs
       - cromwell_outputs
       - cromwell_submit_batch

tests/fixtures/cromwell_labels_data.yml

@@ -0,0 +1,26 @@
+http_interactions:
+- request:
+    method: get
+    uri: http://localhost:8000/api/workflows/v1/287c7902-abc0-49ab-a6ec-0ce0c097b4d2/labels
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      Accept: application/json, text/xml, application/xml, */*
+  response:
+    status:
+      status_code: 200
+      category: Success
+      reason: OK
+      message: 'Success: (200) OK'
+    headers:
+      server: akka-http/10.1.15
+      date: Fri, 26 Jul 2024 19:26:12 GMT
+      content-type: application/json
+      content-length: '200'
+    body:
+      encoding: ''
+      file: no
+      string: '{"id":"287c7902-abc0-49ab-a6ec-0ce0c097b4d2","labels":{"Label":"Apple","secondaryLabel":"Orange","workflowType":"AppSubmission","cromwell-workflow-id":"cromwell-287c7902-abc0-49ab-a6ec-0ce0c097b4d2"}}'
+  recorded_at: 2024-07-26 19:26:12 GMT
+  recorded_with: vcr/1.6.0, webmockr/1.0.0

tests/fixtures/cromwell_labels_submit.yml

@@ -0,0 +1,30 @@
+http_interactions:
+- request:
+    method: post
+    uri: http://localhost:8000/api/workflows/v1
+    body:
+      encoding: ''
+      string: workflowSource=list(path = "/Users/schambe3/github/getwilds/rcromwell/inst/examples/hello.wdl",
+        type = "application/octet-stream", name = NULL),workflowInputs=list(path =
+        "/Users/schambe3/github/getwilds/rcromwell/inst/examples/inputs.json", type
+        = "application/json", name = NULL),labels=list(path = "/private/var/folders/qt/fzq1m_bj2yb_7b2jz57s9q7c0000gp/T/Rtmp21huqY/rcromwell_1609933b0cbaf.json",
+        type = "application/json", name = NULL)
+    headers:
+      Accept: application/json, text/xml, application/xml, */*
+  response:
+    status:
+      status_code: 201
+      category: Success
+      reason: Created
+      message: 'Success: (201) Created'
+    headers:
+      server: akka-http/10.1.15
+      date: Fri, 26 Jul 2024 19:25:52 GMT
+      content-type: application/json
+      content-length: '66'
+    body:
+      encoding: ''
+      file: no
+      string: '{"id":"287c7902-abc0-49ab-a6ec-0ce0c097b4d2","status":"Submitted"}'
+  recorded_at: 2024-07-26 19:25:52 GMT
+  recorded_with: vcr/1.6.0, webmockr/1.0.0

tests/testthat/helper-vcr.R

@@ -15,3 +15,11 @@ file_workflow_opts <- sys_file("examples/workflow_options.json")
 
 # suppress messages for the test run
 cromwell_config(verbose = FALSE)
+
+cromwell_localhost_up <- function() {
+  try8000 <- tryCatch(
+    curl::curl_fetch_memory("localhost:8000"),
+    error = function(e) e
+  )
+  !inherits(try8000, "error")
+}

tests/testthat/test-cromwell_call.R

@@ -10,5 +10,6 @@ test_that("cromwell_call", {
   })
 
   expect_s3_class(res, "data.frame")
+  expect_s3_class(res, "tbl")
   expect_equal(res$callName, "hello")
 })

tests/testthat/test-cromwell_failures.R

@@ -1,7 +1,3 @@
-# FIXME: cromwell_failures doesn't appear to be working. At least for the
-# case where data is in the $failures slot at the top level of the list
-# the parsing code doesn't grab it - perhaps the API response has changed
-
 test_that("cromwell_failures", {
   vcr::use_cassette("cromwell_failures_prep", {
     job <- cromwell_submit_batch(wdl = file_hello, params = file_inputs_bad)

tests/testthat/test-cromwell_jobs.R

@@ -6,6 +6,9 @@ test_that("cromwell_jobs", {
     match_requests_on = c("method", "host", "path")
   )
 
+  expect_s3_class(res, "data.frame")
   expect_s3_class(res, "tbl")
   expect_equal(NCOL(res), 8)
+  # explicit column ordering for better understanding
+  expect_equal(names(res)[1], "workflow_name")
 })

tests/testthat/test-cromwell_labels.R

@@ -0,0 +1,24 @@
+test_that("cromwell_labels", {
+  my_labels <- data.frame(
+    "workflowType" = "AppSubmission",
+    "Label" = "Apple",
+    "secondaryLabel" = "Orange"
+  )
+
+  vcr::use_cassette("cromwell_labels_submit", {
+    res <- cromwell_submit_batch(
+      wdl = file_hello, params = file_inputs,
+      labels = my_labels
+    )
+  })
+
+  # Sys.sleep(20) # Needed only for recording new fixture #nolint
+
+  vcr::use_cassette("cromwell_labels_data", {
+    labels_from_workflow <- cromwell_labels(res$id)
+  })
+
+  expect_length(labels_from_workflow, 4)
+  expect_equal(labels_from_workflow$Label, "Apple")
+  expect_equal(labels_from_workflow$secondaryLabel, "Orange")
+})

tests/testthat/test-error-handling.R

@@ -1,3 +1,5 @@
+skip_if_not(cromwell_localhost_up())
+
 test_that("proof api or DIY cromwell server down", {
   # This should happen whether proof or DIY if not on
   # campus or VPN for Fred Hutch at least