Remove unneeded check

Author: michaelhallquist

NEWS.md

@@ -1,6 +1,7 @@
 # BrainGnomes 0.8-2
 
 * Refactor postprocessing to use job arrays and sentinels for cleanup
+* Add additional templates to prefetch needed by MRIQC
 
 # BrainGnomes 0.8-1
 

R/process_subject.R

@@ -790,7 +790,6 @@ sched_script = NULL, sched_args = NULL, parent_ids = NULL, lg = NULL, pp_stream
     input_dir = input_dir, # postprocess_subject.sbatch will figure out files to postprocess using input and input_regex
     input_regex = pp_cfg$input_regex,
     postprocess_image_sched_script = postprocess_image_sched_script,
-    postprocess_sentinel_sched_script = postprocess_sentinel_sched_script,
     max_concurrent_images = as.character(max_concurrent_images),
     sched_args = sched_args, # pass through to child processes
     stream_name = pp_stream,

inst/hpc_scripts/postprocess_subject.pbs

@@ -40,8 +40,6 @@ ncores=${PBS_NP:-1}
 [ ! -f "$postprocess_image_sched_script" ] && echo "postprocess_image_sched_script $postprocess_image_sched_script not found. Exiting" && exit 1
 [ ! -r "$postprocess_image_sched_script" ] && echo "postprocess_image_sched_script $postprocess_image_sched_script not readable. Exiting" && exit 1
 [ -z "$stream_name" ] && echo "stream_name not set. Exiting" && exit 1
-[ -z "$postprocess_sentinel_sched_script" ] && echo "postprocess_sentinel_sched_script is not set. Exiting" && exit 1
-[ ! -f "$postprocess_sentinel_sched_script" ] && echo "postprocess_sentinel_sched_script $postprocess_sentinel_sched_script not found. Exiting" && exit 1
 
 # Default concurrency limit if not set by caller
 [ -z "$max_concurrent_images" ] && max_concurrent_images=4
@@ -220,4 +218,3 @@ fi
 "${R_HOME}/bin/Rscript" "$upd_job_status_path" --job_id "$PBS_JOBID" --sqlite_db "$sqlite_db" --status "COMPLETED"
 log_message INFO "Postprocess parent job completed for subject $sub_id $ses_str. Array ($array_jid) and sentinel (${sentinel_jid:-unknown}) are running."
 exit 0
-

inst/hpc_scripts/postprocess_subject.sbatch

@@ -40,8 +40,6 @@ ncores=$SLURM_NTASKS
 [ ! -f "$postprocess_image_sched_script" ] && echo "postprocess_image_sched_script $postprocess_image_sched_script not found. Exiting" && exit 1
 [ ! -r "$postprocess_image_sched_script" ] && echo "postprocess_image_sched_script $postprocess_image_sched_script not readable. Exiting" && exit 1
 [ -z "$stream_name" ] && echo "stream_name not set. Exiting" && exit 1
-[ -z "$postprocess_sentinel_sched_script" ] && echo "postprocess_sentinel_sched_script is not set. Exiting" && exit 1
-[ ! -f "$postprocess_sentinel_sched_script" ] && echo "postprocess_sentinel_sched_script $postprocess_sentinel_sched_script not found. Exiting" && exit 1
 
 # Default concurrency limit if not set by caller
 [ -z "$max_concurrent_images" ] && max_concurrent_images=4
@@ -161,4 +159,3 @@ fi
 "${R_HOME}/bin/Rscript" "$upd_job_status_path" --job_id "$SLURM_JOB_ID" --sqlite_db "$sqlite_db" --status "COMPLETED"
 log_message INFO "Postprocess parent job completed for subject $sub_id $ses_str. Array ($array_jid) and sentinel (${sentinel_jid:-unknown}) are running."
 exit 0
-

tests/testthat/test-submit_postprocess-sentinel.R

@@ -86,6 +86,7 @@ test_that("submit_postprocess builds sentinel sched args from the selected strea
 
   expect_identical(job_id, "67890")
   expect_length(calls, 2L)
+  expect_false("postprocess_sentinel_sched_script" %in% names(calls[[1]]$env_variables))
   expect_match(calls[[2]]$sched_args, "--time=00:15:00")
   expect_match(calls[[2]]$sched_args, "--mem=2g")
   expect_match(calls[[2]]$sched_args, "-n 1", fixed = TRUE)