WIP: Updates based on production testing

sequence_processing_pipeline/Job.py

@@ -9,6 +9,7 @@
 import logging
 from inspect import stack
 import re
+from collections import Counter, defaultdict
 
 
 class Job:
@@ -263,24 +264,36 @@ def query_slurm(job_ids):
                 jobs[unique_id] = state
 
                 if unique_id != job_id:
-                    child_jobs[unique_id] = job_id  # job is a child job
+                    # job is a child job
+                    child_jobs[unique_id] = [job_id, state]
 
             return jobs, child_jobs
 
         while True:
             jobs, child_jobs = query_slurm(job_ids)
 
-            for jid in job_ids:
-                logging.debug("JOB %s: %s" % (jid, jobs[jid]))
-                if callback is not None:
-                    callback(jid=jid, status=jobs[jid])
-
-                children = [x for x in child_jobs if child_jobs[x] == jid]
-                if len(children) == 0:
-                    logging.debug("\tNO CHILDREN")
-                for cid in children:
-                    logging.debug("\tCHILD JOB %s: %s" % (cid, jobs[cid]))
-            status = [jobs[x] in Job.slurm_status_not_running for x in job_ids]
+            status = []
+            status_display = defaultdict(list)
+
+            # check main jobs
+            for job in job_ids:
+                status.append(jobs[job] in Job.slurm_status_not_running)
+                status_display[job].append(jobs[job])
+
+            # check children
+            for child_job, (parent_job, state) in child_jobs.items():
+                status_display[parent_job].append(state)
+                status.append(state in Job.slurm_status_not_running)
+
+            if callback is not None:
+                status_text = []
+                for parent_job, state in status_display.items():
+                    msg = ', '.join([f'{x}: {y}' for x, y in
+                                     Counter(state).most_common()])
+                    status_text.append(f'{parent_job}: {msg}')
+
+                # job_id is contained in status_text so jid='' is fine.
+                callback(jid='', status=' -- '.join(status_text))
 
             if set(status) == {True}:
                 # all jobs either completed successfully or terminated.

sequence_processing_pipeline/templates/nuqc_job.sh

@@ -12,6 +12,7 @@
 ### Commented out for now, but there is a possibility it will be needed
 ### in the future.
 ###SBATCH --gres=node_jobs:{{gres_value}}
+#SBATCH --constraint="amd"
 
 
 echo "---------------"