## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(abba)

## ----submit_batch, eval=FALSE-------------------------------------------------
# abba_submit_batch(
#   list(c("/home/mike.stackhouse/test_progs/r_job_test.R",
#          "/home/mike.stackhouse/test_progs/r_job_test2.R"),
#        "/home/mike.stackhouse/test_progs/r_job_test3.R"),
#   submit_func=abba_rslauncher_submit_job_local,
#   wait_func=abba_rslauncher_watch_job_local,
#   log_path="/home/mike.stackhouse/test_logs",
#   timeout_seconds = 15
#   )
# #  /home/yevhenii.boiko/k8s_test/r_job_test.R /home/yevhenii.boiko/k8s_test/r_job_test2.R /home/yevhenii.boiko/k8s_test/r_job_test3.R
# #  "TG9jYWw6UitNSWpxN2FaQ3JyQXRqbGQ5TzVFUT09"  "TG9jYWw6eGVremgtbGRNMFF0VDFFVG5MTEEzdz09"  "TG9jYWw6eENZb2lBR2x1RVJyZVYyelo0Z040QT09"

## ----create_batch_list, eval=FALSE--------------------------------------------
# ds <- as.data.frame(list(program_name=c("/home/yevhenii.boiko/k8s_test/r_job_test.R", "/home/yevhenii.boiko/k8s_test/r_job_test2.R", "/home/yevhenii.boiko/k8s_test/r_job_test3.R"),
#                          inputs=c("raw.DM", "raw.EX,sdtm.DM", "raw.AE,sdtm.DM"),
#                          outputs=c("sdtm.DM", "sdtm.EX", "sdtm.AE")))
# calculate_run_group(ds, col_name='run_group')
# #                                  program_name         inputs outputs run_group
# # 1  /home/yevhenii.boiko/k8s_test/r_job_test.R         raw.DM sdtm.DM         1
# # 2 /home/yevhenii.boiko/k8s_test/r_job_test2.R raw.EX,sdtm.DM sdtm.EX         2
# # 3 /home/yevhenii.boiko/k8s_test/r_job_test3.R raw.AE,sdtm.DM sdtm.AE         2

## ----example_batch_execution, eval=FALSE--------------------------------------
# abba_submit_batch(calculate_run_group(ds, col_name='run_group'),
#                   submit_func=abba_rslauncher_submit_job_local,
#                   wait_func=abba_rslauncher_watch_job_local,
#                   log_path="/home/mike.stackhouse/test_logs"
#   )
# #  /home/yevhenii.boiko/k8s_test/r_job_test.R /home/yevhenii.boiko/k8s_test/r_job_test2.R /home/yevhenii.boiko/k8s_test/r_job_test3.R
# #  "TG9jYWw6UGVPUVFoeVVMKys2c3M0TnZZcm9ZUT09"  "TG9jYWw6VmgrUnlueDBOLXZuVkVIYWxRa1NEZz09"  "TG9jYWw6bGlWcjdsVTRwQzIwcmlLUThzUUN4UT09"

## ----get_batch_log, eval=FALSE------------------------------------------------
# abba_rslauncher_get_job_log_local(c("TG9jYWw6UGVPUVFoeVVMKys2c3M0TnZZcm9ZUT09", "TG9jYWw6VmgrUnlueDBOLXZuVkVIYWxRa1NEZz09", "TG9jYWw6bGlWcjdsVTRwQzIwcmlLUThzUUN4UT09"))
# # [[1]]
# # [1] "[1] \"Program r_job_test start run timestamp: 2024-03-28 16:48:39\"" "[1] \"Program r_job_test end run timestamp: 2024-03-28 16:48:40\""
# # [3] "Warning message:"                                                    "No useful work done here. "
# #
# # [[2]]
# # [1] "[1] \"Program r_job_test2 start run timestamp: 2024-03-28 16:48:41\"" "[1] \"Program r_job_test2 end run timestamp: 2024-03-28 16:48:42\""
# # [3] "Warning message:"                                                     "No useful work done here. "
# #
# # [[3]]
# # [1] "[1] \"Program r_job_test3 start run timestamp: 2024-03-28 16:48:41\"" "[1] \"Program r_job_test3 end run timestamp: 2024-03-28 16:48:42\""
# # [3] "Warning message:"                                                     "No useful work done here. "

## ----example_batch_execution_sequential, eval=FALSE---------------------------
# abba_submit_batch(calculate_run_group(ds, col_name='run_group'),
#                   submit_func=abba_rslauncher_submit_job_local,
#                   wait_func=abba_rslauncher_watch_job_local,
#                   log_path="/home/mike.stackhouse/test_logs",
#                   sequential=TRUE
#   )
# #  /home/yevhenii.boiko/k8s_test/r_job_test.R /home/yevhenii.boiko/k8s_test/r_job_test2.R /home/yevhenii.boiko/k8s_test/r_job_test3.R
# #  "TG9jYWw6cGppOTZSOXgtR3FDbGdpZGtzaVh1UT09"  "TG9jYWw6VlFhVEs4MXNlWmRmOUh1dG9PeEZFZz09"  "TG9jYWw6Um5YbzY5ZEU5bHN0ZlRTMVBZNm1DZz09"
# 
# abba_rslauncher_get_job_log_local(c("TG9jYWw6cGppOTZSOXgtR3FDbGdpZGtzaVh1UT09","TG9jYWw6VlFhVEs4MXNlWmRmOUh1dG9PeEZFZz09","TG9jYWw6Um5YbzY5ZEU5bHN0ZlRTMVBZNm1DZz09" ))
# # [[1]]
# # [1] "[1] \"Program r_job_test start run timestamp: 2024-03-28 16:52:01\"" "[1] \"Program r_job_test end run timestamp: 2024-03-28 16:52:02\""
# # [3] "Warning message:"                                                    "No useful work done here. "
# #
# # [[2]]
# # [1] "[1] \"Program r_job_test2 start run timestamp: 2024-03-28 16:52:04\"" "[1] \"Program r_job_test2 end run timestamp: 2024-03-28 16:52:05\""
# # [3] "Warning message:"                                                     "No useful work done here. "
# #
# # [[3]]
# # [1] "[1] \"Program r_job_test3 start run timestamp: 2024-03-28 16:52:06\"" "[1] \"Program r_job_test3 end run timestamp: 2024-03-28 16:52:07\""
# # [3] "Warning message:"                                                     "No useful work done here. "