run_task: Run the task defined in a conf file

In shinybatch: Launch Tasks in Batch

Description

Run the task defined in a conf file

Usage

run_task(
  conf_path,
  ignore_status = c("running", "finished", "error"),
  save_rds = TRUE,
  compress = TRUE,
  return = TRUE,
  verbose = FALSE
)

Arguments

conf_path	character. Path to the conf file.
ignore_status	character (c("running", "finished", "error")). Status to be ignored when launching tasks.
save_rds	logical Save output in output/res.RDS ? Default to TRUE
compress	logical or character (TRUE). Either a logical specifying whether or not to use "gzip" compression, or one of "gzip", "bzip2" or "xz" to indicate the type of compression to be used.
return	logical Get back result in R ? Default to TRUE
verbose	logical See running task message ? Default to FALSE

Value

the result of the task (function applied on prepared args).

Examples

# create temporary directory for conf
dir_conf <- paste0(tempdir(), "/conf", round(runif(n = 1, max = 10000)))
dir.create(dir_conf, recursive = TRUE)

# ex fun
fun_path = system.file("ex_fun/sb_fun_ex.R", package = "shinybatch")
fun_name = "sb_fun_ex"

# create and save conf
conf <- configure_task(dir_path = dir_conf,
                       conf_descr = list(
                         title = "my_title",
                         description = "my_descr"
                       ),
                       fun_path = fun_path,
                       fun_name = fun_name,
                       fun_args = list(
                         x = 1,
                         y = 0:4,
                         z = iris
                       ),
                       priority = 1)

conf_init <- yaml::read_yaml(paste0(conf$dir, "conf.yml"))
y <- readRDS(paste0(conf$dir, "inputs/y.RDS"))
z <- readRDS(paste0(conf$dir, "inputs/z.RDS"))

run_task(paste0(conf$dir, "conf.yml"))

# catch results
list.files(conf$dir)
conf_update <- yaml::read_yaml(paste0(conf$dir, "conf.yml"))
output <- readRDS(paste0(conf$dir, "output/res.RDS"))
log <- read.delim(list.files(paste0(conf$dir, "output/"),
                             pattern = "log_run", full.names = TRUE), header = FALSE)

shinybatch documentation built on June 30, 2021, 9:06 a.m.