added parallel processing

corpusparser/Parser.py

@@ -3,6 +3,7 @@ import re
 import json
 from lxml import etree
 import logging
+import time
 
 logging.basicConfig(level=logging.INFO)
 
@@ -10,17 +11,13 @@ logging.basicConfig(level=logging.INFO)
 # Create an iterator that outputs resulting sentences (python dict format).  
 class Parser():
 
-    def __init__(self, corpus, infiles, logger=None):
+    def __init__(self, corpus, kres_srl_folder=None, logger=None):
-
-        if corpus == "kres":
-            self.kres_folder = Path(infiles[0])
-            self.kres_srl_folder = Path(infiles[1])
-        elif corpus == "ssj":
-            self.ssj_file = Path(infiles[0])
-        else:
-            raise ValueError("Argument corpus should be 'ssj' or 'kres'.")
 
         self.corpus = corpus
+
+        if self.corpus == "kres":
+            self.kres_srl_folder = kres_srl_folder
+
         self.W_TAGS = ['w']
         self.C_TAGS = ['c']
         self.S_TAGS = ['S', 'pc']
@@ -94,7 +91,7 @@ class Parser():
 
     def sentence_generator(self):
         # Using generators so we don't copy a whole corpu around in memory.
-        # Might be too complicated. Try per-file generator instead. 
+        # Use parse_xml_file() instead for pre-file processing (parallelism?)
         if self.corpus == "kres":
 
             # some logging output
@@ -102,23 +99,23 @@ class Parser():
                 self.n_kres_files = len(list(Path(self.kres_folder).glob('*')))
 
             for xml_file in self.kres_folder.iterdir():
-                # self.parse_xml_file(xml_file)
                 self.nth_kres_file += 1
                 self.logger.info("{} ({}/{})".format(
                     xml_file, self.nth_kres_file, self.n_kres_files))
-                yield from self.parse_xml_file(xml_file)
+                yield from self.xml_file_to_generator(xml_file)
         else:
-            yield from self.parse_xml_file(self.ssj_file)
+            yield from self.xml_file_to_generator(self.ssj_file)
-
-    def kres_to_json_file(self, in_xml_file, out_json_file):
-        out_buffer = []
-        for _, sentence_entry in parser.parser_xml_file(in_xml_file):
-            out_buffer += [sentence_entry]
-
-        with outfile.open("w") as fp:
-            json.dump(out_buffer, fp)
 
     def parse_xml_file(self, xml_file):
+        tstart = time.time()
+        file_data = []
+        for tpl in self.xml_file_to_generator(xml_file):
+            file_data += [tpl[1]]
+        tend = time.time()
+        self.logger.info("Parsed {} in {:.4f} s".format(xml_file, tend - tstart))
+        return file_data
+
+    def xml_file_to_generator(self, xml_file):
         # for separate srl links, it will guess the srl file based on 
         # self.kres_srl_folder
 

corpusparser/main.py

@@ -5,74 +5,30 @@ import logging
 import json
 from pymongo import MongoClient
 import sys
+from multiprocessing import Pool
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-## Main handles command line arguments and writing to files / DB.  
+n_kres_files = -1  # for logging
-
-def ssj_to_json_file(sentence_generator, outfolder):
-    # this funciton is based on the fact that files are parsed sequentially
-    outfolder = Path(outfolder)
-    outfolder.mkdir(parents=True, exist_ok=True)
-    outfile = outfolder / "ssj500k.json"
-
-    data_buffer = []
-    for s in sentence_generator:
-        sdata = s[1]
-        data_buffer += [sdata]
-
-    # outfile = Path(outfile)
-    with outfile.open("w") as fp:
-        logger.info("Writing to {}".format(outfile))
-        json.dump(data_buffer, fp)
-
-def kres_to_json_files(sentence_generator, outfolder):
-    outfolder = Path(outfolder) / "kres_json"
-    outfolder.mkdir(parents=True, exist_ok=True)
-
-    def write_buffer_to_file(outfile, outfile_buffer):
-        logger.info("Writing file: {}".format(outfile))
-        with outfile.open("w") as fp:
-            json.dump(outfile_buffer, fp)
-
-    outfile_buffer = None
-    current_outfile = None
-    for s in sentence_generator:
-        infile = s[0]
-        outfile = outfolder / Path(infile.name.split(".")[0]).with_suffix(".json")
-
-        # parser sequentially parses files; when we're done with a file, write it out
-        if current_outfile is None:
-            current_outfile = outfile
-            outfile_buffer = [] 
-        elif outfile != current_outfile:
-            write_buffer_to_file(current_outfile, outfile_buffer)
-            current_outfile = outfile
-            outfile_buffer = []
-
-        # update buffer
-        sdata = s[1]
-        outfile_buffer += [sdata]
-    write_buffer_to_file(current_outfile, outfile_buffer)
-
-def data_to_valdb(sentence_generator, dbaddr, username, password, collection_name):
-    logger.info("Connecting to: {}".format(dbaddr))
-    client = MongoClient(
-        "mongodb://{}".format(dbaddr),
-        username=username,
-        password=password,
-        authSource="valdb",
-        authMechanism='SCRAM-SHA-1'
-    )
-    valdb = client.valdb
-    logger.info("Writing data to {}.".format(collection_name))
-    col = valdb[collection_name]
-    for s in sentence_generator:
-        sdata = s[1]
-        # col.insert_one(sdata)
-        col.update({"sid": sdata["sid"]}, sdata, upsert=True)
 
+# handler for concurrency
+def _handle_kres_file_tpl(kres_file_tpl):
+    kres_file_idx = kres_file_tpl[0]
+    kres_file = kres_file_tpl[1]
+    logging.info("Handling {} ({}/{})".format(
+        kres_file, kres_file_idx, n_kres_files))
+    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_col = valdb["kres"]
+        for sentence in kres_data:
+            kres_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Parsing corpora kres and ssj500k.")
@@ -84,41 +40,51 @@ if __name__ == "__main__":
     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)
     args = parser.parse_args()
 
-
+    outdir = None
-    # parse ssj
+    valdb = None
-    logger.info("Parsing ssj500k: {}".format(args.ssj_file))
-    ssj_parser = Parser(
-        corpus="ssj",
-        infiles=[args.ssj_file],
-    )
-    # ssj to json
     if args.output == "file":
-        ssj_to_json_file(ssj_parser.sentence_generator(), args.outdir)
+        outdir = Path(args.outdir)
+        outdir.mkdir(parents=True, exist_ok=True)
     elif args.output == "db":
-        data_to_valdb(
+        dbclient = MongoClient(
-            ssj_parser.sentence_generator(),
+            "mongodb://{}".format(args.dbaddr),
-            args.dbaddr,
+            username=args.dbuser,
-            args.dbuser,
+            password=args.dbpass,
-            args.dbpass,
+            authSource="valdb",
-            collection_name="ssj"
+            authMechanism='SCRAM-SHA-1'
         )
+        valdb = dbclient.valdb
 
-    # parse kres
+    # SSJ
-    logger.info("Parsing Kres: {}".format(args.ssj_file))
+    logger.info("Parsing Ssj: {}".format(args.ssj_file))
+    ssj_parser = Parser(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":
+        ssj_col = valdb["ssj"]
+        for sentence in ssj_data:
+            ssj_col.update({"sid": sentence["sid"]}, sentence, upsert=True)
+
+
+    # Kres
+    logger.info("Parsing Kres: {}".format(args.kres_folder))
     kres_parser = Parser(
         corpus="kres",
-        infiles=[args.kres_folder, args.kres_srl_folder],
+        kres_srl_folder=args.kres_srl_folder
     )
-    # kres to json
+
-    if args.output == "file":
+    # [(idx, filepath)]
-        kres_to_json_files(kres_parser.sentence_generator(), args.outdir)
+    kres_files = [x for x in Path(args.kres_folder).iterdir()]
-    elif args.output == "db":
+    kres_files = [x for x in enumerate(kres_files)]
-        data_to_valdb(
+    n_kres_files = len(kres_files)
-            kres_parser.sentence_generator(),
+
-            args.dbaddr,
+    p = Pool(int(args.cores))
-            args.dbuser,
+    p.map(_handle_kres_file_tpl, kres_files)
-            args.dbpass,
+
-            collection_name="kres"
+    logger.info("Finished parsing.")
-        )