updated get_slurm_jobs to prevent error filtering when no jobs are in…

… squeue.
A2-ai · Sep 9, 2024 · 1159134 · 1159134
1 parent 458ca13
commit 1159134
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Showing 4 changed files with 61 additions and 52 deletions.
diff --git a/R/get-jobs.R b/R/get-jobs.R
@@ -56,7 +56,16 @@ get_slurm_jobs <- function(user = NULL){
   res_df$submit_time <- as.POSIXct(res_df$submit_time, origin = "1970-01-01")
   res_df$start_time <- as.POSIXct(res_df$start_time, origin = "1970-01-01")
   if (!is.null(user)) {
-    return(dplyr::filter(res_df, user_name == user))
+    df <- tryCatch(
+      {
+        dplyr::filter(res_df, user_name == user)
+      },
+      error = function(e) {
+        res_df
+      }
+    )
+  } else {
+    df <- res_df
   }
-  res_df
+  return(df)
 }
diff --git a/vignettes/Running-nonmem.Rmd b/vignettes/Running-nonmem.Rmd
@@ -250,20 +250,20 @@ To reiterate, this template file is run as a bash shell script so anything you c
 
 ```{r, include = FALSE}
 #cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```
diff --git a/vignettes/custom-alerts.Rmd b/vignettes/custom-alerts.Rmd
@@ -247,21 +247,21 @@ This gives us the notifications in a much more digestible format
 ![nmm ntfy.sh alerts](data/images/nmm_ntfy_alerts.png)
 
 ```{r, include = FALSE}
-#cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# #cancelling any running nonmem jobs
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```
diff --git a/vignettes/slack-alerts.Rmd b/vignettes/slack-alerts.Rmd
@@ -125,21 +125,21 @@ slurmtools::get_slurm_jobs()
 ![nmm slack alerts](data/images/nmm_slack_notifications.png)
 
 ```{r, include = FALSE}
-#cancelling any running nonmem jobs
-state <- slurmtools::get_slurm_jobs(user = "matthews")
-
-if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-  for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-    processx::run("scancel", args = paste0(job_id))
-  }
-}
-
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
+# #cancelling any running nonmem jobs
+# state <- slurmtools::get_slurm_jobs(user = "matthews")
+# 
+# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
+#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
+#     processx::run("scancel", args = paste0(job_id))
+#   }
+# }
+# 
+# #removing generated files from running this vignette
+# nonmem <- file.path("model", "nonmem")
+# 
+# unlink(file.path(nonmem, "1001"), recursive = TRUE)
+# unlink(file.path(nonmem, "1001.yaml"))
+# unlink(file.path(nonmem, "1001.toml"))
+# unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+# unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```