a

corpusparser/main.py

@@ -9,17 +9,19 @@ import sys
 from multiprocessing import Pool
 import time
 
+CORPORA = ["kres", "ssj"]
+
 # logging.basicConfig(filename=Path("/var/tmp/corpusparser.log"), filemode='a', level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-# lfh = logging.FileHandler("/var/tmp/fill-database.log")
+# lfh = logging.FileHandler("/project/logs/fill-database.log")
 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
 
 
 def enriched_lemma(token):
@@ -49,18 +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),
@@ -69,25 +67,40 @@ 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:
+        try:
+            kres_data = kres_parser.parse_xml_file(kres_file)
+        except:
+            logger.error("Failed to parse file: {}".format(kres_file))
+            continue
+        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":
-        """
+            """
-        for sentence in kres_data:
+            if dbclient.valdb["kres"].find({"sid": kres_data[0]["sid"]}).count() > 0:
-            kres_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+                logger.info("File {} already in DB, closing chunk ({}/{})".format(
-        """
+                    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]
+    try:
-        kres_col.insert_many(kres_data_1)  # much much better (just make sure sid has a unique index)
+        dbclient.valdb["kres"].insert_many(db_payload, ordered=False)  # much much better (just make sure sid has a unique index)
-        logger.info("Inserted data from {} ({}/{}) in {:.2f} s".format(
+    except:
-            kres_file, kres_file_idx, n_kres_files, time.time() - tstart))
+        logger.error("Failed inserting kres files chunk ({}/{}) in {:.2f} s".format(
+            kres_chunk_idx, n_chunks, time.time() - tstart))
+    logger.info("Db insert: chunks ({}/{}) in {:.2f} s".format(
+        kres_chunk_idx, n_chunks, time.time() - tstart))
+    dbclient.close()
 
 def _get_dbclient(args):
     dbclient = MongoClient(
@@ -100,72 +113,79 @@ def _get_dbclient(args):
     return dbclient
 
 
-# wrap it in a function for better garbage collection
-def parse_ssj(args):
-    logger.info("Parsing Ssj: {}".format(args.ssj_file))
-    ssj_parser = Parser(logger=logger, corpus="ssj")
-    ssj_data = ssj_parser.parse_xml_file(Path(args.ssj_file))
-    if args.output == "file":
-        ssj_outfile = outdir / "ssj500k.json"
-        with ssj_outfile.open("w") as fp:
-            json.dump(ssj_data, fp)
-    elif args.output == "db":
-        dbclient = _get_dbclient(args)
-        valdb = dbclient.valdb
-        ssj_col = valdb["ssj"]
-        for sentence in ssj_data:
-            sentence = _db_preprocess(sentence)
-            ssj_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
-    del ssj_parser
-    del ssj_data
-
-
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Parsing corpora kres and ssj500k.")
-    parser.add_argument('--kres-folder', required=True)
+    parser.add_argument('--corpus', required=True)
-    parser.add_argument('--kres-srl-folder', required=True)
+    parser.add_argument('--kres-folder', required=False)
-    parser.add_argument('--ssj-file', required=True)
+    parser.add_argument('--kres-srl-folder', required=False)
+    parser.add_argument('--ssj-file', required=False)
     parser.add_argument('--output', required=False, default=None)
     parser.add_argument('--outdir', required=False, default=None)
     parser.add_argument('--dbaddr', required=False, default=None)
     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()
 
+
+    corpus = args.corpus
+    assert (corpus in CORPORA), "Wrong corpus name."
+
+
     outdir = None
     if args.output == "file":
         outdir = Path(args.outdir)
         outdir.mkdir(parents=True, exist_ok=True)
     elif args.output == "db":
-        # Force unique sid
         dbclient = _get_dbclient(args)
-        for corpus in ["kres", "ssj"]:
+        dbclient.valdb[corpus].ensure_index([("sid", pymongo.ASCENDING)])
-            dbclient.valdb[corpus].ensure_index([("sid", pymongo.ASCENDING)])
+        dbclient.valdb[corpus].ensure_index([("headwords", pymongo.ASCENDING)])
-            dbclient.valdb[corpus].ensure_index([("headwords", pymongo.ASCENDING)])
+        dbclient.valdb[corpus].ensure_index([("functors", pymongo.ASCENDING)])
-            dbclient.valdb[corpus].ensure_index([("functors", pymongo.ASCENDING)])
+        dbclient.close()
 
 
-    # SSJ
+    if corpus == "ssj":
-    p = Pool(1)
+        logger.info("Parsing Ssj: {}".format(args.ssj_file))
-    p.map(parse_ssj, [args])
+        ssj_parser = Parser(logger=logger, corpus="ssj")
+        ssj_data = ssj_parser.parse_xml_file(Path(args.ssj_file))
+        if args.output == "file":
+            ssj_outfile = outdir / "ssj500k.json"
+            with ssj_outfile.open("w") as fp:
+                json.dump(ssj_data, fp)
+        elif args.output == "db":
+            dbclient = _get_dbclient(args)
+            valdb = dbclient.valdb
+            ssj_col = valdb["ssj"]
+            for sentence in ssj_data:
+                sentence = _db_preprocess(sentence)
+                ssj_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+            dbclient.close()
 
-    time.sleep(30)
 
-    # Kres
+    if corpus == "kres":
-    logger.info("Parsing Kres: {}".format(args.kres_folder))
+        # Kres
-    kres_parser = Parser(
+        logger.info("Parsing Kres: {}".format(args.kres_folder))
-        logger=logger,
+        kres_parser = Parser(
-        corpus="kres",
+            logger=logger,
-        kres_srl_folder=args.kres_srl_folder
+            corpus="kres",
-    )
+            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 Path(args.kres_folder).iterdir()]
+        kres_files = sorted(kres_files, key=lambda x: x.name)
-    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_chunk, kres_files_chunks)
 
-    p = Pool(int(args.cores))
-    p.map(_handle_kres_file_tpl, kres_files)
     
     logger.info("Finished parsing.")