cleanup old which eliminates functions

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fh.wdlR
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 1.1.0
+Version: 2.0.0
 Authors@R: 
     person(given = "Amy",
            family = "Paguirigan",

NAMESPACE

@@ -11,9 +11,10 @@ export(cromwellJobs)
 export(cromwellOutputs)
 export(cromwellSubmitBatch)
 export(cromwellTiming)
+export(cromwellValidate)
 export(cromwellVersion)
 export(cromwellWorkflow)
-export(womtoolValidate)
+export(setCromwellURL)
 export(workflowInputs)
 export(workflowOptions)
 importFrom(magrittr,"%>%")

R/womtoolValidate.R → R/cromwellValidate.R

@@ -12,7 +12,7 @@
 #' @examples
 #' TBD
 #' @export
-womtoolValidate <-
+cromwellValidate <-
   function(WDL, allInputs=NULL, cromURL = Sys.getenv("CROMWELLURL", unset = "needsURL")) {
     if(cromURL == "needsURL") {
       stop("CROMWELLURL is not set in your environment, or specify the URL to query via cromURL.")

R/setCromwellURL.R

@@ -1,67 +1,13 @@
-#' Set CROMWELLURL variable based on a gizmo SLURM jobId
+#' Set the URL for your Cromwell server's API
 #'
 #'
-#' @param FredHutchId Your Fred Hutch username
-#' @param jobId The SLURM job id for your Cromwell server
-#' @param port The port you specified in your Cromwell config file (`fh-slurm-cromwell.config`), default is "2020" from the template here: https://github.com/FredHutch/diy-cromwell-server.
-#' @param local Are you running this on your local machine (TRUE) or on the rhino's (FALSE)
+#' @param nodeAndPort Your node and port of the running Cromwell server on Gizmo (e.g., gizmoz85:12345)
 #' @return Sets your environment variable CROMWELLURL to be that of the Cromwell server for the job specified.
 #' @author Amy Paguirigan
-#' @details
-#' Will require your Fred Hutch Id and will prompt you to enter your Fred Hutch password.
-#' NOTE:  this function has been dicontinued due to setting up Cromwell in a more secure way.
-setCromwellURL <- function(FredHutchId = NULL, jobId = NULL, port = "2020", local = TRUE) {
-  if (is.null(FredHutchId) == T) {
-    stop("Please supply your Fred Hutch id.")
+#' @export
+setCromwellURL <- function(nodeAndPort = NULL) {
+  if (is.null(nodeAndPort) == T) {
+    stop("Please supply the node and port of your Cromwell server.")
   }
-  if (is.null(jobId) == T) {
-    stop("Please supply the SLURM jobId of your Cromwell server job.")
-  }
-
-  rhino <- "@rhino03" # remove this once bionic shift allows it
-
-  nodecommand = paste0('squeue -o "%R" -j ', jobId)
-
-  if (local == T){
-  # Make an ssh session to rhino and it will prompt for password
-  session <- ssh::ssh_connect(paste0(FredHutchId, rhino))
-  getNode <- ssh::ssh_exec_internal(session, command = nodecommand)
-  nodeName <- sub("^.*)", "", gsub("\n", "", rawToChar(getNode$stdout)))
-  if (nodeName == ""){
-    message("Re-querying for node name.")
-    Sys.sleep(2)
-    getNode <- ssh::ssh_exec_internal(session, command = nodecommand)
-    nodeName <- sub("^.*)", "", gsub("\n", "", rawToChar(getNode$stdout)))
-    if (nodeName == ""){
-      ssh::ssh_disconnect(session)
-      stop("Your job likely has not yet been assigned a node yet.  Please use
-             `squeue -u <username>` on `rhino` to find out if your job has been
-             assigned or use the function `setCromwellURL()` in this package.")
-      }
-    }
-  }
-  if (local == F) {
-    getNode <- system(command = nodecommand, intern = TRUE)
-    nodeName <- getNode[3]
-    if (nodeName %in% c("", " ")){
-      message("Re-querying for node name.")
-      Sys.sleep(2)
-      getNode <- system(command = nodecommand, intern = TRUE)
-      nodeName <- getNode[3]
-      if (nodeName == ""){
-        stop("Your job likely has not yet been assigned a node yet.  Please use
-             `squeue -u <username>` on `rhino` to find out if your job has been
-             assigned or use the function `setCromwellURL()` in this package.")
-      }
-    }
-  }
-
-  message(paste0("Your Cromwell server is on node: ", nodeName))
-  message(paste0("To use the Swagger UI in a Browser, go to: http://", nodeName, ":", port))
-
-  Sys.setenv(CROMWELLURL=paste0("http://", nodeName, ":", port))
-  message(paste0("CROMWELLURL is currently set to: ", Sys.getenv("CROMWELLURL")))
-
-  ssh::ssh_disconnect(session)
-  return(list(jobId = jobId, cromwellURL = paste0("http://", nodeName, ":", port)))
+  Sys.setenv(CROMWELLURL=paste0("http://", nodeAndPort))
 }