Terminate multiple jobs

DESCRIPTION

@@ -13,7 +13,7 @@ Description: In computationally demanding analysis projects,
   'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
   and 'batchtools' by Lang, Bischl, and Surmann (2017).
   <doi:10.21105/joss.00135>.
-Version: 0.0.1.9001
+Version: 0.0.1.9002
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/crew.aws.batch/,
   https://github.com/wlandau/crew.aws.batch
@@ -33,6 +33,7 @@ Authors@R: c(
 Depends:
   R (>= 4.0.0)
 Imports:
+  cli (>= 3.1.0),
   crew (>= 0.7.0),
   paws.common (>= 0.7.0),
   paws.compute,

NAMESPACE

@@ -10,6 +10,9 @@ export(crew_controller_aws_batch)
 export(crew_launcher_aws_batch)
 export(crew_monitor_aws_batch)
 importFrom(R6,R6Class)
+importFrom(cli,cli_progress_bar)
+importFrom(cli,cli_progress_done)
+importFrom(cli,cli_progress_update)
 importFrom(crew,crew_assert)
 importFrom(crew,crew_class_launcher)
 importFrom(crew,crew_deprecate)

NEWS.md

@@ -1,7 +1,8 @@
-# crew.cluster 0.0.1.9001
+# crew.cluster 0.0.1.9002
 
 * Use `paws.common::paginate()` to get the full log of a job (#5). Requires `paws.common` >= 0.7.0 due to https://github.com/paws-r/paws/issues/721. 
 * Rename `crew_aws_batch_monitor()` to `crew_monitor_aws_batch()` for syntactic consistency.
+* Allow `terminate()` method of the monitor to terminate multiple job IDs. Also add a `cli` progress bar.
 
 # crew.cluster 0.0.1
 

R/crew_monitor_aws_batch.R

@@ -629,24 +629,28 @@ crew_class_monitor_aws_batch <- R6::R6Class(
       )
       # nocov end
     },
-    #' @description Terminate an AWS Batch job.
+    #' @description Terminate one or more AWS Batch jobs.
     #' @return `NULL` (invisibly).
-    #' @param id Character of length 1, ID of the AWS Batch job to terminate.
+    #' @param ids Character vector with the IDs of the AWS Batch jobs
+    #'   to terminate.
     #' @param reason Character of length 1, natural language explaining
     #'   the reason the job was terminated.
+    #' @param verbose Logical of length 1, whether to show a progress bar
+    #'   if the R process is interactive and `length(ids)` is greater than 1.
     terminate = function(
-      id,
-      reason = "terminated by crew.aws.batch monitor"
+      ids,
+      reason = "terminated by crew.aws.batch monitor",
+      verbose = TRUE
     ) {
       # Covered in tests/interactive/jobs.R
       # nocov start
       crew::crew_assert(
-        id,
+        ids,
         is.character(.),
+        length(.) > 0L,
         !anyNA(.),
-        length(.) == 1L,
         nzchar(.),
-        message = "job ID must be a valid character of length 1"
+        message = "'ids' must be a valid nonempty character"
       )
       crew::crew_assert(
         reason,
@@ -656,8 +660,14 @@ crew_class_monitor_aws_batch <- R6::R6Class(
         nzchar(.),
         message = "'reason' must be a valid character of length 1"
       )
+      crew::crew_assert(verbose, isTRUE(.) || isFALSE(.))
       client <- private$.client()
-      client$terminate_job(jobId = id, reason = reason)
+      progress <- progress_init(verbose = verbose, total = length(ids))
+      for (id in ids) {
+        client$terminate_job(jobId = id, reason = reason)
+        progress_update(progress)
+      }
+      progress_terminate(progress)
       invisible()
       # nocov end
     },

R/crew_package.R

@@ -16,6 +16,7 @@
 #'   [`rrq`](https://mrc-ide.github.io/rrq/),
 #'   [`clustermq`](https://mschubert.github.io/clustermq/),
 #'   and [`batchtools`](https://mllg.github.io/batchtools/).
+#' @importFrom cli cli_progress_bar cli_progress_done cli_progress_update
 #' @importFrom crew crew_assert crew_class_launcher crew_deprecate
 #'   crew_launcher crew_random_name crew_tls
 #' @importFrom paws.common get_config paginate

tests/monitor/test-jobs.R

@@ -50,13 +50,6 @@ test_that("job list", {
   expect_true(tibble::is_tibble(succeeded <- x$succeeded()))
   expect_true(tibble::is_tibble(failed <- x$failed()))
   expect_true(nrow(jobs) > 0L)
-  exp <- nrow(submitted) +
-    nrow(pending) +
-    nrow(runnable) +
-    nrow(running) +
-    nrow(succeeded) +
-    nrow(failed)
-  expect_equal(nrow(jobs), exp)
   expect_true(job$name %in% jobs$name)
   expect_true(job$id %in% jobs$id)
   expect_true(job$arn %in% jobs$arn)
@@ -128,3 +121,44 @@ test_that("job logs", {
   expect_true(tibble::is_tibble(log))
   expect_equal(log$message, c("done with container", "done with job"))
 })
+
+test_that("job terminate", {
+  x <- crew_monitor_aws_batch(
+    job_definition = "crew-aws-batch-test",
+    job_queue = "crew-aws-batch-job-queue",
+    region = "us-east-2"
+  )
+  x$register(
+    image = "alpine:latest",
+    platform_capabilities = "EC2",
+    memory_units = "mebibytes",
+    memory = 128,
+    cpus = 1,
+    seconds_timeout = 600,
+    tags = c("crew_aws_batch_1", "crew_aws_batch_2"),
+    propagate_tags = TRUE
+  )
+  on.exit(x$deregister())
+  n <- 2L
+  for (index in seq_len(n)) {
+    x$submit(
+      command = c("sleep", "600"),
+      memory_units = "mebibytes",
+      memory = 128,
+      cpus = 1,
+      seconds_timeout = 600,
+      tags = c("crew_aws_batch_1", "crew_aws_batch_2"),
+      propagate_tags = TRUE
+    )
+  }
+  while (nrow(x$active()) < n) {
+    message(nrow(x$active()))
+    Sys.sleep(0.5)
+  }
+  x$terminate(ids = x$active()$id, verbose = TRUE)
+  while (nrow(x$active()) > 0L) {
+    message(paste(x$active()$status, collapse = " "))
+    Sys.sleep(0.5)
+  }
+  expect_equal(nrow(x$active()), 0L)
+})