fix array jobs

Author: mllg

R/submitJobs.R

@@ -276,9 +276,8 @@ submitJobs = function(ids = NULL, resources = list(), sleep = NULL, reg = getDef
       submit = reg$cluster.functions$submitJob(reg = reg, jc = jc)
 
       if (submit$status == 0L) {
-        if (!testString(submit$batch.id, na.ok = FALSE)) {
-          print(str(submit))
-          stopf("Cluster function did not return a valid batch.id")
+        if (!testCharacter(submit$batch.id, any.missing = FALSE, min.len = 1L)) {
+          stopf("Cluster function did not return valid batch ids:\n%s", stri_flatten(capture.output(str(submit$batch.id)), "\n"))
         }
         reg$status[ids.chunk,
           c("submitted", "started", "done",   "error",       "mem.used", "resource.id",         "batch.id",      "log.file",      "job.hash") :=

tests/testthat/test_JobCollection.R

@@ -62,3 +62,11 @@ test_that("makeJobCollection.ExperimentCollection", {
 
   expect_is(jc, "ExperimentCollection")
 })
+
+test_that("chunks.as.arrayjobs is stored", {
+  reg = makeTestRegistry(file.dir = NA, make.default = FALSE)
+  ids = batchMap(identity, 1:2, reg = reg)
+  resources = list(chunks.as.arrayjobs = TRUE)
+  jc = makeJobCollection(ids, resources = resources, reg = reg)
+  expect_true(jc$array.jobs)
+})

tests/testthat/test_submitJobs.R

@@ -27,7 +27,7 @@ test_that("submitJobs", {
   expect_equal(uniqueN(reg$status$job.hash), 2)
 })
 
-test_that("submitJobs: per job resources", {
+test_that("per job resources", {
   reg = makeTestRegistry()
 
   fun = function(...) list(...)
@@ -45,3 +45,13 @@ test_that("submitJobs: per job resources", {
   ids$chunk = 1L
   expect_error(submitJobs(ids, reg = reg), "per-job")
 })
+
+test_that("chunks.as.arrayjobs is passed down", {
+  reg = makeTestRegistry()
+  fun = function(...) list(...)
+  ids = batchMap(fun, i = 1:3, reg = reg)
+  ids$chunk = 1L
+  submitJobs(ids, resources = resources, reg = reg)
+
+
+})