fix when columns don't exist.

getwilds · Mar 4, 2020 · cc188ab · cc188ab
1 parent ac63a6a
commit cc188ab
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/R/cromwellCall.R b/R/cromwellCall.R
@@ -88,11 +88,13 @@ cromwellCall <- function(workflow_id) {
         } else {
           # if end doesn't exist or it is already NA (???), make it and workflowDuration but set to NA
           justCalls$end <- NA
-          justCalls$callDuration <- NA
+          justCalls$callDuration <- 0
         }
       } else {
         # if start doesn't exist, then create it and set it to NA
         justCalls$start <- NA
+        justCalls$end <- NA
+        justCalls$callDuration <- 0
       }
       justCalls <- dplyr::mutate_all(justCalls, as.character)
       justCalls$callDuration <- as.numeric(justCalls$callDuration)

diff --git a/R/cromwellWorkflow.R b/R/cromwellWorkflow.R
@@ -110,11 +110,14 @@ cromwellWorkflow <- function(workflow_id) {
         } else {
           # if end doesn't exist or it is already NA (???), make it and workflowDuration but set to NA
           resultdf$end <- NA
-          resultdf$workflowDuration <- NA
+          resultdf$workflowDuration <- 0
         }
       } else {
         # if start doesn't exist, then create it and set it to NA
         resultdf$start <- NA
+        # if start doesn't exist, then probably end and workflow Duration don't either.
+        resultdf$end <- NA
+        resultdf$workflowDuration <- 0
       }
       resultdf <- dplyr::mutate_all(resultdf, as.character)
       resultdf$workflowDuration <-