time zones are hard.

getwilds · May 8, 2020 · d8b55c5 · d8b55c5
1 parent e3d322c
commit d8b55c5
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Showing 4 changed files with 21 additions and 21 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fh.wdlR
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: 
     person(given = "Amy",
            family = "Paguirigan",
@@ -16,7 +16,8 @@ Imports:
     purrr,
     paws,
     tidyr,
-    ssh
+    ssh,
+    lubridate
 License: GPL-3
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE)

diff --git a/R/cromwellCall.R b/R/cromwellCall.R
@@ -77,18 +77,16 @@ cromwellCall <- function(workflow_id) {
       ## Big Chunk of dealing with start and end times.
       if ("start" %in% colnames(justCalls) == T) {
         # if the workflow has started
-        justCalls$start <-
-          as.POSIXct(justCalls$start, tz = "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
+        justCalls$start <- lubridate::with_tz(lubridate::ymd_hms(justCalls$start), tzone = "US/Pacific")
         if ("end" %in% colnames(justCalls) == T) {
           # and if end is present
-          justCalls$end <-
-            as.POSIXct(justCalls$end, tz = "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
+          justCalls$end <-lubridate::with_tz(lubridate::ymd_hms(justCalls$end), tzone = "US/Pacific")
           justCalls <-
             dplyr::mutate(justCalls, callDuration = round(difftime(end, start, units = "mins"), 3))
         } else {
           # if end doesn't exist or it is already NA (???), make it and workflowDuration but set to NA
           justCalls$end <- NA
-          justCalls$callDuration <- 0
+          justCalls$callDuration <- round(difftime(lubridate::now(tz = "US/Pacific"), justCalls$start, units = "mins"),3)
         }
       } else {
         # if start doesn't exist, then create it and set it to NA

diff --git a/R/cromwellJobs.R b/R/cromwellJobs.R
@@ -31,19 +31,20 @@ cromwellJobs <- function(days = 1) {
     cromTable <- dplyr::rename(cromTable, "workflow_id" = "id")
     if ("end" %in% colnames(cromTable) == T &
         "start" %in% colnames(cromTable) == T) {
-      cromTable$start <-
-        as.POSIXct(cromTable$start, "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
-      cromTable$end <-
-        as.POSIXct(cromTable$end, "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
-      cromTable$submission <-
-        as.character(as.POSIXct(cromTable$submission, "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 )# because PST/hack)
+      cromTable$start <-lubridate::with_tz(lubridate::ymd_hms(cromTable$start), tzone = "US/Pacific")
+      cromTable$end <-lubridate::with_tz(lubridate::ymd_hms(cromTable$end), tzone = "US/Pacific")
+      cromTable$submission <-lubridate::with_tz(lubridate::ymd_hms(cromTable$submission), tzone = "US/Pacific")
       cromTable$workflowDuration <-
         round(difftime(cromTable$end, cromTable$start, units = "mins"),
               3)
       cromTable$workflowDuration <-
         as.numeric(cromTable$workflowDuration)
+    } else if ("start" %in% colnames(cromTable) == T) {
+      cromTable$start <-lubridate::with_tz(lubridate::ymd_hms(cromTable$start), tzone = "US/Pacific")
+      # If it hasn't ended yet, then report the amount of time it's been running to that moment.
+      cromTable$workflowDuration <- round(difftime(Sys.time(), resultdf$start, units = "mins"),3)
     } else {
-      cromTable$workflowDuration <- "NA"
+      cromTable$workflowDuration <- 0
     }
   } else {
     cromTable <- data.frame("workflow_id" = NA,

diff --git a/R/cromwellWorkflow.R b/R/cromwellWorkflow.R
@@ -86,14 +86,12 @@ cromwellWorkflow <- function(workflow_id) {
           purrr::reduce(list(remainder, drag, submit), dplyr::full_join, by = "workflow_id")
       }
       #resultdf <- dplyr::mutate_all(resultdf, as.character)
-      resultdf$submission <-
-        as.character(as.POSIXct(resultdf$submission, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 )# because PST/hack)
+      resultdf$submission <- lubridate::with_tz(lubridate::ymd_hms(resultdf$submission), tzone = "US/Pacific")
       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$start, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
+          resultdf$start <- lubridate::with_tz(lubridate::ymd_hms(resultdf$start), tzone = "US/Pacific")
         } else {
           # if start is NA, then make sure it's set to NA????  Stupid.
           resultdf$start <- NA
@@ -102,15 +100,17 @@ cromwellWorkflow <- function(workflow_id) {
           # and if end is present
           if (is.na(resultdf$end) == F) {
             # and it is not NA
-            resultdf$end <-
-              as.POSIXct(resultdf$end, tz= "UTC", "%Y-%m-%dT%H:%M:%S") - 8*60*60 # because PST/hack
+            resultdf$end <-lubridate::with_tz(lubridate::ymd_hms(resultdf$end), tzone = "US/Pacific")
             resultdf <-
               dplyr::mutate(resultdf, workflowDuration = round(difftime(end, start, units = "mins"), 3))
           }
         } else {
           # if end doesn't exist or it is already NA (???), make it and workflowDuration but set to NA
           resultdf$end <- NA
-          if (is.na(resultdf$start)==F){resultdf$workflowDuration <- as.POSIXct(Sys.time())- resultdf$start} else {
+          if (is.na(resultdf$start)==F){
+            resultdf$workflowDuration <-
+            round(difftime(Sys.time(), resultdf$start, units = "mins"),3)
+            } else {
             resultdf$workflowDuration <- 0}
         }
       } else {