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getwilds · Feb 8, 2024 · b610be5 · b610be5
1 parent e2e65c6
commit b610be5
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Showing 9 changed files with 29 additions and 17 deletions.
diff --git a/R/cromUtils.R b/R/cromUtils.R
@@ -15,7 +15,8 @@
 workflow_options <- function(workflow_id, url = cw_url(), token = NULL) {
   check_url(url)
   dplyr::as_tibble(
-    jsonlite::fromJSON(cromwell_workflow(workflow_id, url, token)$options))
+    jsonlite::fromJSON(cromwell_workflow(workflow_id, url, token)$options)
+  )
 }
 
 #' Pull the workflow inputs provided for a Cromwell workflow job
@@ -29,5 +30,6 @@ workflow_options <- function(workflow_id, url = cw_url(), token = NULL) {
 workflow_inputs <- function(workflow_id, url = cw_url(), token = NULL) {
   check_url(url)
   dplyr::as_tibble(
-    jsonlite::fromJSON(cromwell_workflow(workflow_id, url, token)$inputs))
+    jsonlite::fromJSON(cromwell_workflow(workflow_id, url, token)$inputs)
+  )
 }
diff --git a/R/cromwellAbort.R b/R/cromwellAbort.R
@@ -10,6 +10,7 @@ cromwell_abort <- function(workflow_id, url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg("Aborting job in Cromwell")
   http_post(make_url(url, "api/workflows/v1", workflow_id, "abort"),
-    token = token) %>%
+    token = token
+  ) %>%
     dplyr::as_tibble()
 }
diff --git a/R/cromwellCall.R b/R/cromwellCall.R
@@ -1,3 +1,5 @@
+# nolint start
+
 #' Retrieve metadata for the calls made in a Cromwell workflow job
 #'
 #' Retrieve and process call metadata for a specific workflow.
@@ -252,3 +254,4 @@ cromwell_call <- function(workflow_id, url = cw_url(), token = NULL) {
   }
   return(just_calls)
 }
+# nolint end
diff --git a/R/cromwellGlob.R b/R/cromwellGlob.R
@@ -19,9 +19,9 @@
 #' thisWorkflowID <- recentJobs$workflow_id[1]
 #' workflowMeta <- cromwell_glob(workflow_id = thisWorkflowID)
 #' }
-cromwell_glob <- function(workflow_id, expand_sub_workflows = FALSE,
-  url = cw_url(), token = NULL) {
-
+cromwell_glob <- function(
+    workflow_id, expand_sub_workflows = FALSE,
+    url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg(paste0("Querying for metadata for workflow id: ", workflow_id))
   url <- make_url(url, "api/workflows/v1", workflow_id, "metadata")

diff --git a/R/cromwellJobs.R b/R/cromwellJobs.R
@@ -36,14 +36,16 @@ cromwell_jobs <- function(days = 1,
   }
   crom_dat <-
     http_get(make_url(url, "api/workflows/v1/query"),
-      query = query, token = token)$results
+      query = query, token = token
+    )$results
   cr_table <- purrr::map_dfr(crom_dat, dplyr::bind_rows)
   if (nrow(cr_table) > 0 && "id" %in% names(cr_table)) {
     cr_table <- dplyr::rename(cr_table, "workflow_id" = "id")
     if ("name" %in% colnames(cr_table)) {
       cr_table <- dplyr::rename(cr_table, "workflow_name" = "name")
     }
-    cr_table$submission <- lubridate::with_tz(lubridate::ymd_hms(cr_table$submission),
+    cr_table$submission <- lubridate::with_tz(
+      lubridate::ymd_hms(cr_table$submission),
       tzone = pkg_env$tzone
     )
     if ("start" %in% colnames(cr_table)) {

diff --git a/R/cromwellOutputs.R b/R/cromwellOutputs.R
@@ -46,8 +46,10 @@ cromwell_outputs <- function(workflow_id, url = cw_url(), token = NULL) {
     }
     df$workflow_id <- workflow_id
   } else {
-    df <- dplyr::tibble("workflow_id" =
-                          "No outputs available for this workflow yet")
+    df <- dplyr::tibble(
+      "workflow_id" =
+        "No outputs available for this workflow yet"
+    )
   }
   return(df)
 }
diff --git a/R/cromwellValidate.R b/R/cromwellValidate.R
@@ -11,9 +11,9 @@
 #' @template serverdeets
 #' @return Returns the response from the API post which includes the workflow
 #' ID that you'll need to monitor the job.
-cromwell_validate <- function(wdl, all_inputs = NULL,
-  url = cw_url(), token = NULL) {
-
+cromwell_validate <- function(
+    wdl, all_inputs = NULL,
+    url = cw_url(), token = NULL) {
   check_url(url)
   crom_mssg("Validating a workflow for Cromwell")
 

diff --git a/R/http.R b/R/http.R
@@ -31,7 +31,6 @@ make_url <- function(base_url, ...) {
 #' @param x a url. default: NULL
 #' @keywords internal
 check_url <- function(x = NULL) {
-
   if (identical(x, "") || is.null(x)) {
     stop("Set the env var `CROMWELLURL`. ",
       "See ?cromwell_settings",

diff --git a/tests/testthat/test-cromwell_jobs.R b/tests/testthat/test-cromwell_jobs.R
@@ -1,7 +1,10 @@
 test_that("cromwell_jobs", {
-  vcr::use_cassette("cromwell_jobs", {
-    res <- cromwell_jobs()
-  }, match_requests_on = c("method", "host", "path"))
+  vcr::use_cassette("cromwell_jobs",
+    {
+      res <- cromwell_jobs()
+    },
+    match_requests_on = c("method", "host", "path")
+  )
 
   expect_s3_class(res, "tbl")
   expect_equal(NCOL(res), 8)