More comments on pool for annotation step

PanACoTA/annotate_module/prokka_prodigal_functions.py

@@ -51,8 +51,9 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
     -------
     dict
         {genome: boolean} -> with True if prokka/prodigal ran well, False otherwise.
-    # """
+    """
 
+    # Update information according to annotation soft used and write message
     if prodigal_only:
         message = "Annotating all genomes with prodigal"
         run_annot = run_prodigal
@@ -62,8 +63,10 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
         run_annot = run_prokka
         main_logger = logging.getLogger("qc_annotate.prokka")
     main_logger.info(message)
+    # Get total number of genomes to annotate, used to show annotation progress
     nbgen = len(genomes)
     bar = None
+    # If user did not ask for quiet, create progressbar
     if not quiet:
         # Create progress bar
         widgets = ['Annotation: ', progressbar.Bar(marker='█', left='', right=''),
@@ -72,6 +75,9 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
                   ]
         bar = progressbar.ProgressBar(widgets=widgets, max_value=nbgen,
                                       term_width=100).start()
+    # Get resource availability:
+    # - number of threads used by prokka/prodigal (cores_annot)
+    # - how many genomes can be annotated at the same time (pool_size)
     if threads <= 3:
         cores_annot = threads
         pool_size = 1
@@ -84,33 +90,60 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
         else:
             cores_annot = 2
         pool_size = int(threads / cores_annot)
+    #  Create pool with a given size (=number of tasks to be launched in parallel)
     pool = multiprocessing.Pool(pool_size)
     # Create a Queue to put logs from processes, and handle them after from a single thread
     m = multiprocessing.Manager()
     q = m.Queue()
-    # {genome: [name, gpath_cut_gembase, size, nbcont, l90]}
-    # arguments : (gpath, annot_folder, threads, name, force, nbcont, q) for each genome
-    arguments = [(genomes[g][1], annot_folder, cores_annot, genomes[g][0],
-                  force, genomes[g][3], small, q)
+    # {genome: [gembase_name, path_to_origfile, path_toannotate_file, gsize, nbcont, L90]}
+    # arguments: gpath, prok_folder, threads, name, force, nbcont, small(for prodigal), q
+    arguments = [(genomes[g][2], annot_folder, cores_annot, genomes[g][0],
+                  force, genomes[g][4], small, q)
                  for g in sorted(genomes)]
     try:
+        # Start pool (run 'run_annot' n each set of arguments)
         final = pool.map_async(run_annot, arguments, chunksize=1)
+        # Close pool: no more data will be put on this pool
         pool.close()
         # Listen for logs in processes
         lp = threading.Thread(target=utils.logger_thread, args=(q,))
         lp.start()
         if not quiet:
             while True:
+                # Final is ready when all pool elements are done
                 if final.ready():
                     break
+                # If not done, get number of genomes left
                 remaining = final._number_left
+                # Update progress bar
                 bar.update(nbgen - remaining)
+            # End progress bar
             bar.finish()
         pool.join()
+        # Put None to tell 'q' that everything is finished. It can stopped and be joined.
         q.put(None)
+        # join lp (tell to stop once all log processes are done, which is the case here)
         lp.join()
         final = final.get()
-    # If an error occurs, terminate pool and exit
+
+    # # If user stops programm (ctrl+C), end it
+    # except KeyboardInterrupt as ki:
+    #     print("error")
+    #     for worker in pool._pool:
+    #         print(worker.is_alive())
+    #     pool.join()
+    #     print("closed")
+    #     pool.terminate()
+    #     print("--------------terminate ok----------------")
+    #     lp.join()
+    #     print("thread stopped")
+    #     # run_event.clear()
+    #     # lp.terminate()
+    #     # print("--------------JOIN--------------")
+    #     # pool.terminate()
+    #     main_logger.error("Process killed by CTRL+C")
+    #     return "coucou"
+    # If an error occurs, terminate pool, write error and exit
     except Exception as excp:  # pragma: no cover
         pool.terminate()
         main_logger.error(excp)
@@ -153,10 +186,13 @@ def run_prokka(arguments):
     root.addHandler(qh)
     logger = logging.getLogger('run_prokka')
     logger.log(utils.detail_lvl(), "Start annotating {} {} with Prokka".format(name, gpath))
+
     # Define prokka directory and logfile, and check their existence
     prok_dir = os.path.join(prok_folder, os.path.basename(gpath) + "-prokkaRes")
     fnull = open(os.devnull, 'w')
     prok_logfile = os.path.join(prok_folder, os.path.basename(gpath) + "-prokka.log")
+    # import sys
+    # sys.exit(1)
     # If result dir already exists, check if we can use it or next step or not
     if os.path.isdir(prok_dir) and not force:
         logger.warning(("Prokka results folder already exists.").format(prok_dir))