models/task.py: Launch process only when pre-process completed

In theory the process could have been launched (and has been, see vdj#684) before the pre-process starts
(when it is QUEUED or ASSIGNED). Now we only allow to start it when the pre-process has been completed
(if it has been defined).

Closes #3289

server/web2py/applications/vidjil/models/task.py

@@ -117,7 +117,7 @@ def schedule_run(id_sequence, id_config, grep_reads=None):
     task = scheduler.queue_task(program, args,
                                 repeats = 1, timeout = defs.TASK_TIMEOUT)
     
-    if db.sequence_file[id_sequence].pre_process_flag == "WAIT" or db.sequence_file[id_sequence].pre_process_flag == "RUN" : 
+    if db.sequence_file[id_sequence].pre_process_flag != "COMPLETED" and db.sequence_file[id_sequence].pre_process_flag :
         db.scheduler_task[task.id] = dict(status ="STOPPED")
     
     db.results_file[data_id] = dict(scheduler_task_id = task.id)
@@ -152,7 +152,7 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
     from datetime import timedelta as timed
     
     ## re schedule if pre_process is still pending
-    if db.sequence_file[id_file].pre_process_flag == "WAIT" or db.sequence_file[id_file].pre_process_flag == "RUN" :
+    if db.sequence_file[id_file].pre_process_flag != "COMPLETED" and db.sequence_file[id_file].pre_process_flag:
         
         print("Pre-process is still pending, re-schedule")