processing kres files in chunks to reduce number of DB connections

corpusparser/main.py

@@ -14,14 +14,14 @@ CORPORA = ["kres", "ssj"]
 # logging.basicConfig(filename=Path("/var/tmp/corpusparser.log"), filemode='a', level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-lfh = logging.FileHandler("/project/logs/fill-database.log")
+# lfh = logging.FileHandler("/project/logs/fill-database.log")
-# lfh = logging.StreamHandler(sys.stdout)
+lfh = logging.StreamHandler(sys.stdout)
 formatter = logging.Formatter("%(asctime)s %(levelname)s %(message)s")
 lfh.setFormatter(formatter)
 logger.addHandler(lfh)
 logger.setLevel(logging.INFO)
 
-n_kres_files = -1  # for logging
+n_chunks = -1  # for logging
 
 
 def enriched_lemma(token):
@@ -51,18 +51,14 @@ def _db_preprocess(e):
 
 
 # handler for concurrency
-def _handle_kres_file_tpl(kres_file_tpl):
+def _handle_kres_file_chunk(kres_file_chunk):
     tstart = time.time()
-    kres_file_idx = kres_file_tpl[0]
+    kres_chunk_idx = kres_file_chunk[0]
-    kres_file = kres_file_tpl[1]
+    kres_chunk = kres_file_chunk[1]
-    kres_data = kres_parser.parse_xml_file(kres_file)
+
-    if args.output == "file":
+    dbclient = None
-        kres_outdir = outdir / "kres_json"
+    db_payload = []
-        kres_outdir.mkdir(parents=True, exist_ok=True)
+    if args.output == "db":
-        kres_outfile = kres_outdir / Path(kres_file.name.split(".")[0]).with_suffix(".json")
-        with kres_outfile.open("w") as fp:
-            json.dump(kres_data, fp)
-    elif args.output == "db":
         # mongoclient needs to be created after forking
         dbclient = MongoClient(
             "mongodb://{}".format(args.dbaddr),
@@ -71,25 +67,29 @@ def _handle_kres_file_tpl(kres_file_tpl):
             authSource="valdb",
             authMechanism='SCRAM-SHA-1'
         )
-        valdb = dbclient.valdb
+        # dbclient.valdb["kres"]
-        kres_col = valdb["kres"]
+    for kres_file in kres_chunk:
+        kres_data = kres_parser.parse_xml_file(kres_file)
+        if args.output == "file":
+            kres_outdir = outdir / "kres_json"
+            kres_outdir.mkdir(parents=True, exist_ok=True)
+            kres_outfile = kres_outdir / Path(kres_file.name.split(".")[0]).with_suffix(".json")
+            with kres_outfile.open("w") as fp:
+                json.dump(kres_data, fp)
 
-        # HUUUUGE BOTTLENECK
+        elif args.output == "db":
-        """
+            if dbclient.valdb["kres"].find({"sid": kres_data[0]["sid"]}).count() > 0:
-        for sentence in kres_data:
+                logger.info("File {} already in DB, closing chunk ({}/{})".format(
-            kres_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+                    kres_file, kres_chunk_idx, n_chunks))
-        """
+                dbclient.close()
+                return
 
-        # skip if one of the sentences is already in DB
+            kres_data_1 = [_db_preprocess(x) for x in kres_data]
-        if kres_col.find({"sid": kres_data[0]["sid"]}).count() > 0:
+            db_payload += kres_data_1
-            logger.info("File {} already in DB ({}/{})".format(
-                kres_file, kres_file_idx, n_kres_files))
-            return
 
-        kres_data_1 = [_db_preprocess(x) for x in kres_data]
+        dbclient.valdb["kres"].insert_many(db_payload)  # much much better (just make sure sid has a unique index)
-        kres_col.insert_many(kres_data_1)  # much much better (just make sure sid has a unique index)
+        logger.info("Inserted kres files chunk ({}/{}) in {:.2f} s".format(
-        logger.info("Inserted data from {} ({}/{}) in {:.2f} s".format(
+            kres_chunk_idx, n_chunks, time.time() - tstart))
-            kres_file, kres_file_idx, n_kres_files, time.time() - tstart))
         dbclient.close()
 
 def _get_dbclient(args):
@@ -115,6 +115,7 @@ if __name__ == "__main__":
     parser.add_argument('--dbuser', required=False, default=None)
     parser.add_argument('--dbpass', required=False, default=None)
     parser.add_argument('--cores', required=False, default=1)
+    parser.add_argument('--chunk-size', required=False, default=3)
     args = parser.parse_args()
 
 
@@ -161,13 +162,19 @@ if __name__ == "__main__":
             kres_srl_folder=args.kres_srl_folder
         )
 
-        # [(idx, filepath)]
         kres_files = [x for x in Path(args.kres_folder).iterdir()]
-        kres_files = [x for x in enumerate(kres_files)]
+        kres_files_chunks = []
-        n_kres_files = len(kres_files)
+        i = 0
+        while i < len(kres_files):
+            # kres_files_chunks += kres_files[i:(i+args.chunk_size)]
+            new_i = i + int(args.chunk_size)
+            kres_files_chunks += [kres_files[i:new_i]]
+            i = new_i
+        kres_files_chunks = [x for x in enumerate(kres_files_chunks)]
+        n_chunks = len(kres_files_chunks)
 
         p = Pool(int(args.cores))
-        p.map(_handle_kres_file_tpl, kres_files)
+        p.map(_handle_kres_file_chunk, kres_files_chunks)
 
     
     logger.info("Finished parsing.")