a

corpusparser/Parser.py

@@ -5,7 +5,7 @@ from lxml import etree
 import logging
 import time
 
-logging.basicConfig(level=logging.INFO)
+# logging.basicConfig(level=logging.INFO)
 
 # Read input file(.xml, .json; kres or ssj500k).  
 # Create an iterator that outputs resulting sentences (python dict format).  
@@ -61,7 +61,10 @@ class Parser():
 
     def parse_any_links_ssj(self, sent_el, links_type):
         lgrps = sent_el.findall(".//linkGrp")
+        try:
             links = [x for x in lgrps if x.get("type") == links_type][0]
+        except:
+            return []
         res_links = []
         for link in links:
             tar = self.parse_ssj_target_arg(link.get("target"))

corpusparser/__init__.py

@@ -1 +1,2 @@
 from corpusparser.Parser import Parser
+from corpusparser.main import enriched_lemma

corpusparser/main.py

@@ -9,10 +9,23 @@ import sys
 from multiprocessing import Pool
 import time
 
-logging.basicConfig(level=logging.INFO)
+CORPORA = ["kres", "ssj"]
+
+# logging.basicConfig(filename=Path("/var/tmp/corpusparser.log"), filemode='a', level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-n_kres_files = -1  # for logging
+# 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_chunks = -1
+
+
+def enriched_lemma(token):
+    return (token["lemma"] if token["msd"][0] == "G" else token["lemma"] + "_")
 
 
 def _helper_tid_to_token(tid, tokens):
@@ -29,7 +42,7 @@ def _db_preprocess(e):
     else:
         hw_tids = list(set([x["from"] for x in e["srl_links"]]))
         hw_tokens = [_helper_tid_to_token(tid, e["tokens"]) for tid in hw_tids]
-        headwords = [(t["lemma"] if t["msd"][0] == "G" else t["lemma"] + "_") for t in hw_tokens]
+        headwords = [enriched_lemma(t) for t in hw_tokens]
         e["headwords"] = headwords
 
         functors = list(set([x["afun"] for x in e["srl_links"]]))
@@ -38,18 +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_file = kres_file_tpl[1]
-    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)
-    elif args.output == "db":
+    kres_chunk_idx = kres_file_chunk[0]
+    kres_chunk = kres_file_chunk[1]
+
+    dbclient = None
+    db_payload = []
+    if args.output == "db":
         # mongoclient needs to be created after forking
         dbclient = MongoClient(
             "mongodb://{}".format(args.dbaddr),
@@ -58,19 +67,40 @@ def _handle_kres_file_tpl(kres_file_tpl):
             authSource="valdb",
             authMechanism='SCRAM-SHA-1'
         )
-        valdb = dbclient.valdb
-        kres_col = valdb["kres"]
+        # dbclient.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:
-            kres_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+            if dbclient.valdb["kres"].find({"sid": kres_data[0]["sid"]}).count() > 0:
+                logger.info("File {} already in DB, closing chunk ({}/{})".format(
+                    kres_file, kres_chunk_idx, n_chunks))
+                dbclient.close()
+                return
             """
 
             kres_data_1 = [_db_preprocess(x) for x in kres_data]
-        kres_col.insert_many(kres_data_1)  # much much better (just make sure sid has a unique index)
-        logging.info("Handled {} ({}/{}) in {:.2f} s".format(
-            kres_file, kres_file_idx, n_kres_files, time.time() - tstart))
+            db_payload += kres_data_1
+
+    try:
+        dbclient.valdb["kres"].insert_many(db_payload, ordered=False)  # much much better (just make sure sid has a unique index)
+    except:
+        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(
@@ -82,34 +112,42 @@ def _get_dbclient(args):
     )
     return dbclient
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Parsing corpora kres and ssj500k.")
-    parser.add_argument('--kres-folder', required=True)
-    parser.add_argument('--kres-srl-folder', required=True)
-    parser.add_argument('--ssj-file', required=True)
+    parser.add_argument('--corpus', required=True)
+    parser.add_argument('--kres-folder', required=False)
+    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([("headwords", pymongo.ASCENDING)])
         dbclient.valdb[corpus].ensure_index([("functors", pymongo.ASCENDING)])
+        dbclient.close()
 
-    # SSJ
+
+    if corpus == "ssj":
         logger.info("Parsing Ssj: {}".format(args.ssj_file))
-    ssj_parser = Parser(corpus="ssj")
+        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"
@@ -122,21 +160,32 @@ if __name__ == "__main__":
             for sentence in ssj_data:
                 sentence = _db_preprocess(sentence)
                 ssj_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+            dbclient.close()
 
 
+    if corpus == "kres":
         # Kres
         logger.info("Parsing Kres: {}".format(args.kres_folder))
         kres_parser = Parser(
+            logger=logger,
             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 enumerate(kres_files)]
-    n_kres_files = len(kres_files)
+        kres_files = sorted(kres_files, key=lambda x: x.name)
+        kres_files_chunks = []
+        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.")