Merge pull request #47 from getwilds/dev

Dev changes into main for new rcromwell release
getwilds · Aug 8, 2024 · c58df3d · c58df3d
2 parents 87d1266 + de95ee8
commit c58df3d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rcromwell
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 3.2.4
+Version: 3.2.5
 Authors@R: c(
     person("Amy", "Paguirigan", role = "aut",
            comment = c(ORCID = "0000-0002-6819-9736")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -20,7 +20,9 @@ export(cw_url)
 export(workflow_inputs)
 export(workflow_options)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,any_of)
 importFrom(dplyr,as_tibble)
+importFrom(dplyr,relocate)
 importFrom(dplyr,tibble)
 importFrom(glue,glue)
 importFrom(httr,GET)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,10 @@
-# rcromwell 3.2.4
+# 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
 

diff --git a/R/cromwellCall.R b/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
diff --git a/R/cromwellJobs.R b/R/cromwellJobs.R
@@ -104,5 +104,12 @@ 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)
 }
diff --git a/R/rcromwell-package.R b/R/rcromwell-package.R
@@ -3,7 +3,7 @@
 
 ## usethis namespace: start
 #' @importFrom glue glue
-#' @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
 ## usethis namespace: end

diff --git a/README.Rmd b/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
diff --git a/README.md b/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
diff --git a/tests/testthat/test-cromwell_call.R b/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")
 })
diff --git a/tests/testthat/test-cromwell_failures.R b/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)

diff --git a/tests/testthat/test-cromwell_jobs.R b/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")
 })