Update Time zone and Bionic

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fh.wdlR
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 0.0.3
+Version: 0.1.0
 Authors@R: 
     person(given = "Amy",
            family = "Paguirigan",

R/cromwellCreate.R

@@ -9,7 +9,7 @@
 #' @param pathToParams Full path in our file system to where you have saved the parameters you'd like your Cromwell server to use (e.g. cromwellParams.sh, https://github.com/FredHutch/diy-cromwell-server).
 #' @param pathToConfig Full path in our file system to where you have saved the configuration file you'd like your Cromwell server to use (e.g. fh-slurm-cromwell.conf, 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 cluster Optional: if present, specify the cluster of the server, either 'gizmo' or other cluster name.
+#' @param cluster Optional: default is trusty, and will submit to rhino nodes, while bionic will connect to rhino03 to submit to Bionic nodes.
 #' @return Sets your environment variable CROMWELLURL to be that of the Cromwell server you just started and returns the information about the job ID and node you'll need.
 #' @author Amy Paguirigan
 #' @details
@@ -26,7 +26,8 @@ cromwellCreate <- function(FredHutchId = NULL, port = "2020",
                            pathToServerScript = NULL,
                            pathToParams = NULL,
                            pathToConfig = NULL,
-                           cluster = "gizmo", local = TRUE) {
+                           cluster = "trusty",
+                           local = TRUE) {
   if (is.null(FredHutchId) == T) {
     stop("Please supply your Fred Hutch id.")
   }
@@ -42,10 +43,13 @@ cromwellCreate <- function(FredHutchId = NULL, port = "2020",
   if (is.null(pathToConfig) == T) {
     stop("Please supply the full path to where the configuration file is saved (e.g., fh-slurm-cromwell.conf).")
   }
+  if (cluster == "trusty") { rhino <- "@rhino"
+  } else if (cluster == "bionic") { rhino <- "@rhino03"
+  } else { stop("You specified 'cluster' as neither 'trusty' nor 'bionic', so I'm not sure which 'rhino' to submit your request to.")}
 
   if (local == T){
   # Make an ssh session to rhino and it will prompt for password
-  session <- ssh::ssh_connect(paste0(FredHutchId, "@rhino"))
+  session <- ssh::ssh_connect(paste0(FredHutchId, rhino))
   # send the command to gizmo to start your server and save the response
   setupServer <- ssh::ssh_exec_internal(session,
                                    command = paste("sbatch", "-o",
@@ -62,7 +66,7 @@ cromwellCreate <- function(FredHutchId = NULL, port = "2020",
     ssh::ssh_disconnect(session)
     stop("Slurm Job ID is unset.")
   }
-  nodecommand = paste0('squeue -M ', cluster, ' -o "%R" -j ', slurmJob)
+  nodecommand = paste0('squeue -o "%R" -j ', slurmJob)
   Sys.sleep(2)
   getNode <- ssh::ssh_exec_internal(session, command = nodecommand)
   nodeName <- sub("^.*)", "", gsub("\n", "", rawToChar(getNode$stdout)))
@@ -94,7 +98,7 @@ cromwellCreate <- function(FredHutchId = NULL, port = "2020",
     if(slurmJob == ""){
       stop("Slurm Job ID is unset.")
     }
-    nodecommand = paste0('squeue -M ', cluster, ' -o "%R" -j ', slurmJob)
+    nodecommand = paste0('squeue -o "%R" -j ', slurmJob)
     Sys.sleep(2)
     getNode <- system(command = nodecommand, intern = TRUE)
     nodeName <- getNode[3]

R/cromwellWorkflow.R

@@ -87,13 +87,13 @@ cromwellWorkflow <- function(workflow_id) {
       }
       #resultdf <- dplyr::mutate_all(resultdf, as.character)
       resultdf$submission <-
-        as.character(as.POSIXct(resultdf$submission, tz= "America/Los_Angeles", "%Y-%m-%dT%H:%M:%S") - 7*60*60 )# because PST/hack)
+        as.character(as.POSIXct(resultdf$submission, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 )# because PST/hack)
       if ("start" %in% colnames(resultdf) == T) {
         # if the workflow has started
         if (is.na(resultdf$start) == F) {
           # and if the value of start is not NA
           resultdf$start <-
-            as.POSIXct(resultdf$start, tz= "America/Los_Angeles", "%Y-%m-%dT%H:%M:%S") - 7*60*60 # because PST/hack
+            as.POSIXct(resultdf$start, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
         } else {
           # if start is NA, then make sure it's set to NA????  Stupid.
           resultdf$start <- NA
@@ -103,7 +103,7 @@ cromwellWorkflow <- function(workflow_id) {
           if (is.na(resultdf$end) == F) {
             # and it is not NA
             resultdf$end <-
-              as.POSIXct(resultdf$end, tz= "America/Los_Angeles", "%Y-%m-%dT%H:%M:%S") - 7*60*60 # because PST/hack
+              as.POSIXct(resultdf$end, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
             resultdf <-
               dplyr::mutate(resultdf, workflowDuration = round(difftime(end, start, units = "mins"), 3))
           }

R/setCromwellURL.R

@@ -5,27 +5,29 @@
 #' @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 cluster Optional: if present, specify the location of the server, either 'gizmo' or 'beagle'
+#' @param cluster Optional: default is trusty, and will submit to rhino nodes, while bionic will connect to rhino03 to submit to Bionic nodes.
 #' @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.
 #' @export
-setCromwellURL <- function(FredHutchId = NULL, jobId = NULL, port = "2020", local = TRUE, cluster = "gizmo") {
+setCromwellURL <- function(FredHutchId = NULL, jobId = NULL, port = "2020", local = TRUE, cluster = "trusty") {
   if (is.null(FredHutchId) == T) {
     stop("Please supply your Fred Hutch id.")
   }
   if (is.null(jobId) == T) {
     stop("Please supply the SLURM jobId of your Cromwell server job.")
   }
-  if (cluster == "gizmo"){
-    nodecommand = paste0('squeue -M gizmo -o "%R" -j ', jobId)
-  } else if (cluster == "beagle"){
-    nodecommand = paste0('squeue -M beagle -o "%R" -j ', jobId)
-  }
+
+  if (cluster == "trusty") { rhino <- "@rhino"
+  } else if (cluster == "bionic") { rhino <- "@rhino03"
+  } else { stop("You specified 'cluster' as neither 'trusty' nor 'bionic', so I'm not sure which 'rhino' to submit your request to.")}
+
+  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"))
+  session <- ssh::ssh_connect(paste0(FredHutchId, rhino))
   getNode <- ssh::ssh_exec_internal(session, command = nodecommand)
   nodeName <- sub("^.*)", "", gsub("\n", "", rawToChar(getNode$stdout)))
   if (nodeName == ""){