Disable wait for fasta generation on compressed fasta, it's always too long

lib/functions.py

@@ -198,12 +198,12 @@ class Functions:
         if compress:
             Functions.compress(fasta_file_o)
         os.remove(lock_file)
-        if mailer is not None:
+        if mailer is not None and not os.path.exists(lock_file + ".pending"):
             Functions.send_fasta_ready(mailer, job_name, sample_name, compress)
 
     @staticmethod
     def compress_and_send_mail(job_name, fasta_file, index_file, lock_file, compressed, mailer):
         Functions.compress(fasta_file)
+        os.remove(lock_file)
         index, sample_name = Functions.read_index(index_file)
         Functions.send_fasta_ready(mailer, job_name, sample_name, compressed)
-        os.remove(lock_file)

srv/main.py

@@ -215,6 +215,8 @@ def build_fasta(id_res):
         if is_sorted and not query_fasta.endswith(".sorted"):
             # Do the sort
             Path(lock_query).touch()
+            if not compressed:  # If compressed, it will took a long time, so not wait
+                Path(lock_query + ".pending").touch()
             thread = threading.Timer(1, Functions.sort_fasta, kwargs={
                 "job_name": id_res,
                 "fasta_file": query_fasta,
@@ -224,7 +226,19 @@ def build_fasta(id_res):
                 "mailer": mailer
             })
             thread.start()
-            return jsonify({"success": True, "status": 0, "status_message": "Started"})
+            if not compressed:
+                i = 0
+                time.sleep(5)
+                while os.path.exists(lock_query) and i < 2:
+                    i += 1
+                    time.sleep(5)
+                if os.path.exists(lock_query):
+                    os.remove(lock_query + ".pending")
+                    return jsonify({"success": True, "status": 1, "status_message": "In progress"})
+                return jsonify({"success": True, "status": 2, "status_message": "Done",
+                                "gzip": query_fasta.endswith(".gz") or query_fasta.endswith(".gz.sorted")})
+            else:
+                return jsonify({"success": True, "status": 1, "status_message": "In progress"})
         elif is_sorted and os.path.exists(lock_query):
             # Sort is already in progress
             return jsonify({"success": True, "status": 1, "status_message": "In progress"})