Merge pull request #45 from getwilds/dev

new fxn cromwell_labels

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: rcromwell
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 3.2.2.91
+Version: 3.2.4
 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: https://getwilds.org/rcromwell/, https://github.com/getwilds/rcromwell
+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:
@@ -24,7 +24,7 @@ License: MIT + file LICENSE
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
     "roxyglobals::global_roclet"))
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Suggests:
     curl,

NAMESPACE

@@ -8,6 +8,7 @@ export(cromwell_config)
 export(cromwell_failures)
 export(cromwell_glob)
 export(cromwell_jobs)
+export(cromwell_labels)
 export(cromwell_logs)
 export(cromwell_outputs)
 export(cromwell_submit_batch)

NEWS.md

@@ -1,3 +1,7 @@
+# rcromwell 3.2.4
+
+* gains new function `cromwell_labels` that hits the `/labels` route (#43) (#45)
+
 # rcromwell 3.2.1
 
 * fix `cromwell_submit_batch` - internally changed `workflow_options` to `workflowOptions` (#32)

R/cromwellOutputs.R

@@ -34,7 +34,9 @@ cromwell_outputs_query <- function(workflow_id, url = cw_url(), token = NULL) {
 
 #' @autoglobal
 cromwell_outputs_process <- function(resp, workflow_id) {
-  if (length(resp$outputs) == 0) return(dplyr::tibble())
+  if (length(resp$outputs) == 0) {
+    return(dplyr::tibble())
+  }
   # grab only the outputs list and unlist into a dataframe
   df <- purrr::map_dfr(resp$outputs, function(x) {
     z <- dplyr::tibble("pathToOutput" = unlist(x))

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/labels.R

@@ -0,0 +1,22 @@
+#' Cromwell labels for a workflow
+#'
+#' @export
+#' @template workflowid
+#' @template serverdeets
+#' @return a named list of workflow labels
+cromwell_labels <- function(workflow_id, url = cw_url(), token = NULL) {
+  check_url(url)
+  response <- http_get(
+    url = make_url(
+      url,
+      "api/workflows/v1",
+      workflow_id,
+      "labels"
+    ),
+    as = "parsed",
+    token = token
+  )
+  labels <- response$labels
+  names(labels)[grep("cromwell-workflow-id", names(labels))] <- "workflow_id"
+  labels
+}

_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_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