styling changes

- change all fxn names from camelCase to snake_case
- change all or at least most internal variables from camelCase to snake_case
- not set in stone in our guide yet but I intend for us to use snake_case across all getwilds pkgs
-

NAMESPACE

@@ -1,22 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(cromwellAbort)
-export(cromwellBackends)
-export(cromwellCache)
-export(cromwellCall)
-export(cromwellConfig)
-export(cromwellFailures)
-export(cromwellGlob)
-export(cromwellJobs)
-export(cromwellOutputs)
-export(cromwellSubmitBatch)
-export(cromwellTiming)
-export(cromwellValidate)
-export(cromwellVersion)
-export(cromwellWorkflow)
-export(workflowInputs)
-export(workflowOptions)
+export(cromwell_abort)
+export(cromwell_backends)
+export(cromwell_cache)
+export(cromwell_call)
+export(cromwell_config)
+export(cromwell_failures)
+export(cromwell_glob)
+export(cromwell_jobs)
+export(cromwell_outputs)
+export(cromwell_submit_batch)
+export(cromwell_timing)
+export(cromwell_validate)
+export(cromwell_version)
+export(cromwell_workflow)
+export(workflow_inputs)
+export(workflow_options)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,tibble)
 importFrom(magrittr,"%>%")

R/cromUtils.R

@@ -7,22 +7,22 @@
 #' Requires valid Cromwell server URL to be set. See [cromwellSettings]
 #' @export
 #' @examples \dontrun{
-#' jobs <- cromwellJobs()
-#' workflowOptions(jobs$workflow_id[1])
+#' jobs <- cromwell_jobs()
+#' workflow_options(jobs$workflow_id[1])
 #' }
-workflowOptions <- function(workflow_id) {
+workflow_options <- function(workflow_id) {
   check_url()
-  dplyr::as_tibble(jsonlite::fromJSON(cromwellWorkflow(workflow_id)$options))
+  dplyr::as_tibble(jsonlite::fromJSON(cromwell_workflow(workflow_id)$options))
 }
 
 #' Pull the workflow inputs provided for a Cromwell workflow job
 #'
 #' @template workflowid
 #' @return Returns a data frame of the inputs for a workflow previously run
 #' @author Amy Paguirigan
-#' @inheritSection workflowOptions Important
+#' @inheritSection workflow_options Important
 #' @export
-workflowInputs <- function(workflow_id) {
+workflow_inputs <- function(workflow_id) {
   check_url()
-  dplyr::as_tibble(jsonlite::fromJSON(cromwellWorkflow(workflow_id)$inputs))
+  dplyr::as_tibble(jsonlite::fromJSON(cromwell_workflow(workflow_id)$inputs))
 }

R/cromwellAbort.R

@@ -3,11 +3,11 @@
 #' @template workflowid
 #' @return Returns the response from the API post
 #' @author Amy Paguirigan
-#' @inheritSection workflowOptions Important
+#' @inheritSection workflow_options Important
 #' @export
-cromwellAbort <- function(workflow_id) {
+cromwell_abort <- function(workflow_id) {
   check_url()
   crom_mssg("Aborting job in Cromwell")
-  httpPOST(url = make_url("api/workflows/v1", workflow_id, "abort")) %>%
+  http_post(url = make_url("api/workflows/v1", workflow_id, "abort")) %>%
     dplyr::as_tibble()
 }

R/cromwellBackends.R

@@ -2,12 +2,12 @@
 #'
 #' @return Cromwell backend options
 #' @author Amy Paguirigan
-#' @inheritSection workflowOptions Important
+#' @inheritSection workflow_options Important
 #' @export
-cromwellBackends <- function() {
+cromwell_backends <- function() {
   check_url()
   crom_mssg("Getting backend options from Cromwell")
-  all <- httpGET(make_url("api/workflows/v1/backends"))
+  all <- http_get(make_url("api/workflows/v1/backends"))
   all$supportedBackends <- unlist(all$supportedBackends)
   return(all)
 }

R/cromwellCache.R

@@ -7,17 +7,17 @@
 #' workflow. NOTE: Currently does not support subworkflows well.
 #' @author Amy Paguirigan
 #' @autoglobal
-#' @inheritSection workflowOptions Important
+#' @inheritSection workflow_options Important
 #' @export
-cromwellCache <- function(workflow_id) {
+cromwell_cache <- function(workflow_id) {
   check_url()
   crom_mssg(paste0(
     "Querying for call caching metadata for workflow id: ",
     workflow_id
   ))
 
   crommetadata <-
-    httpGET(
+    http_get(
       url = make_url("api/workflows/v1", workflow_id, "metadata"),
       query = list(expandSubWorkflows = "false"),
       as = "parsed"
@@ -26,35 +26,35 @@ cromwellCache <- function(workflow_id) {
   if (length(crommetadata$calls) > 0) {
     # if there are calls to be queried, continue
     # we only want the calls data from the metadata for this workflow
-    bobCalls <- purrr::pluck(crommetadata, "calls")
-    bobCallMeta <-
-      purrr::map(bobCalls, function(callData) {
+    bob_calls <- purrr::pluck(crommetadata, "calls")
+    bob_call_meta <-
+      purrr::map(bob_calls, function(call_data) {
         # for each of the calls in the workflow...
-        purrr::map_dfr(callData, function(shardData) {
+        purrr::map_dfr(call_data, function(shard_data) {
           # and for each of the shards in that workflow...
-          if ("inputs" %in% names(shardData)) {
+          if ("inputs" %in% names(shard_data)) {
             a <- purrr::keep(
-              shardData,
-              names(shardData) %in% c("callCaching", "inputs", "outputs")
+              shard_data,
+              names(shard_data) %in% c("callCaching", "inputs", "outputs")
             ) # select only these lists
             # flatten them and make them a data frame
             b <- dplyr::as_tibble(rbind(unlist(a)))
             # add the shard Index associated
-            b$shardIndex <- shardData$shardIndex
+            b$shardIndex <- shard_data$shardIndex
           } else {
-            b <- dplyr::as_tibble("shardIndex" = shardData$shardIndex)
+            b <- dplyr::as_tibble("shardIndex" = shard_data$shardIndex)
           }
           b$shardIndex <- as.character(b$shardIndex)
           b$workflow_id <- workflow_id
-          b$executionStatus <- shardData$executionStatus
-          b$returnCode <- shardData$returnCode
-          b$jobId <- shardData$jobId
+          b$executionStatus <- shard_data$executionStatus
+          b$returnCode <- shard_data$returnCode
+          b$jobId <- shard_data$jobId
           # then remove any data from the messy hitFailures lists
           b <- dplyr::select(b, -dplyr::starts_with("callCaching.hitFailures"))
           return(b)
         })
       })
-    geocache <- purrr::map_dfr(bobCallMeta, rbind, .id = "fullName")
+    geocache <- purrr::map_dfr(bob_call_meta, rbind, .id = "fullName")
     # split fullname into workflowName and callName
     geocache <- tidyr::separate(
       data = geocache,