From: Nathan TeBlunthuis Date: Sun, 17 Oct 2021 20:22:22 +0000 (-0700) Subject: initial work on parquet support X-Git-Url: https://code.communitydata.science/mediawiki_dump_tools.git/commitdiff_plain/d8d20f670b98507a3dea27c38e5463c1b0b2e6cd?hp=cdfa77d66ddc5b0af9fad3b30da7bbe2530ce3bc initial work on parquet support --- diff --git a/wikiq b/wikiq index 0543a33..c2a2f12 100755 --- a/wikiq +++ b/wikiq @@ -24,6 +24,13 @@ PERSISTENCE_RADIUS=7 from deltas import SequenceMatcher from deltas import SegmentMatcher +from dataclasses import dataclass +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq + +from typing import List + class PersistMethod: none = 0 sequence = 1 @@ -174,44 +181,87 @@ class RegexPair(object): # there are no capture groups, we just search for all the matches of the regex else: #given that there are matches to be made - if self.pattern.search(content) is not None: - m = self.pattern.findall(content) - temp_dict[self.label] = ', '.join(m) - else: - temp_dict[self.label] = None + if type(content) in(str, bytes): + if self.pattern.search(content) is not None: + m = self.pattern.findall(content) + temp_dict[self.label] = ', '.join(m) + else: + temp_dict[self.label] = None + # update rev_data with our new columns rev_data.update(temp_dict) return rev_data - +@dataclass +class RevData(): + revid: int + date_time: datetime + articleid: int + editorid: int + title: str + namespace: int + deleted: bool + text_chars: int + revert: bool + reverteds: list[bool] + sha1: str + text_chars: int + revert: bool + reverteds: list[int] + minor: bool + editor: str + anon: bool + collapsed_revs:int + token_revs:int + tokens_added:int + tokens_removed:int + tokens_window:int + class WikiqParser(): - def __init__(self, input_file, output_file, regex_match_revision, regex_match_comment, regex_revision_label, regex_comment_label, collapse_user=False, persist=None, urlencode=False, namespaces = None, revert_radius=15): + def __init__(self, input_file, output_file, regex_match_revision, regex_match_comment, regex_revision_label, regex_comment_label, collapse_user=False, persist=None, urlencode=False, namespaces = None, revert_radius=15, output_parquet=True, parquet_buffer_size=2000): """ Parameters: persist : what persistence method to use. Takes a PersistMethod value """ self.input_file = input_file - self.output_file = output_file + self.collapse_user = collapse_user self.persist = persist self.printed_header = False self.namespaces = [] self.urlencode = urlencode self.revert_radius = revert_radius + + self.parquet_buffer = [] + self.parquet_buffer_size = parquet_buffer_size if namespaces is not None: self.namespace_filter = set(namespaces) else: self.namespace_filter = None + self.regex_schemas = [] self.regex_revision_pairs = self.make_matchmake_pairs(regex_match_revision, regex_revision_label) self.regex_comment_pairs = self.make_matchmake_pairs(regex_match_comment, regex_comment_label) - + + + if output_parquet is True: + self.output_parquet = True + self.pq_writer = None + self.output_file = output_file + else: + self.output_file = open(output_file,'w') + def make_matchmake_pairs(self, patterns, labels): if (patterns is not None and labels is not None) and \ (len(patterns) == len(labels)): - return [RegexPair(pattern, label) for pattern, label in zip(patterns, labels)] + result = [] + for pattern, label in zip(patterns, labels): + result.append(RegexPair(pattern, label)) + self.regex_schemas.append(pa.field(label, pa.list_(pa.string()))) + + return result elif (patterns is None and labels is None): return [] else: @@ -301,7 +351,7 @@ class WikiqParser(): 'revid':rev.id, 'date_time' : rev.timestamp.strftime('%Y-%m-%d %H:%M:%S'), 'articleid' : page.id, - 'editor_id' : "" if rev.deleted.user == True or rev.user.id is None else rev.user.id, + 'editorid' : "" if rev.deleted.user == True or rev.user.id is None else rev.user.id, 'title' : '"' + page.title + '"', 'namespace' : namespace, 'deleted' : "TRUE" if rev.deleted.text else "FALSE" @@ -411,7 +461,6 @@ class WikiqParser(): rev_data["tokens_added"] = num_tokens rev_data["tokens_removed"] = len(tokens_removed) rev_data["tokens_window"] = len(window)-(i+1) - self.print_rev_data(rev_data) page_count += 1 @@ -419,22 +468,65 @@ class WikiqParser(): print("Done: %s revisions and %s pages." % (rev_count, page_count), file=sys.stderr) + if self.output_parquet is True: + self.flush_parquet_buffer() + self.pq_writer.close() + + else: + output_file.close() + + + def write_parquet_row(self, rev_data): + if 'deleted' in rev_data.keys(): + rev_data['deleted'] = True if rev_data['deleted'] == "TRUE" else False + + if 'minor' in rev_data.keys(): + rev_data['minor'] = True if rev_data['minor'] == "TRUE" else False + + + if 'anon' in rev_data.keys(): + rev_data['anon'] = True if rev_data['anon'] == "TRUE" else False + + + self.parquet_buffer.append(rev_data) + + if len(self.parquet_buffer) >= self.parquet_buffer_size: + self.flush_parquet_buffer() + + def flush_parquet_buffer(self): + outtable = pd.DataFrame.from_records(self.parquet_buffer) + outtable = pa.Table.from_pandas(outtable) + if self.pq_writer is None: + schema = outtable.schema + for regex_schema in self.regex_schemas: + schema.append(regex_schema) + + self.pq_writer = pq.ParquetWriter(self.output_file, schema, flavor='spark') + + self.pq_writer.write_table(outtable) + def print_rev_data(self, rev_data): + + if self.output_parquet is False: + printfunc = lambda rev_data: print("\t".join(rev_data), file=self.output_file) + else: + printfunc = self.write_parquet_row + # if it's the first time through, print the header if self.urlencode: for field in TO_ENCODE: rev_data[field] = quote(str(rev_data[field])) if not self.printed_header: - print("\t".join([str(k) for k in sorted(rev_data.keys())]), file=self.output_file) + printfunc(rev_data) self.printed_header = True - print("\t".join([str(v) for k, v in sorted(rev_data.items())]), file=self.output_file) + printfunc(rev_data) def open_input_file(input_filename): if re.match(r'.*\.7z$', input_filename): - cmd = ["7za", "x", "-so", input_filename, '*'] + cmd = ["7za", "x", "-so", input_filename, "*.xml"] elif re.match(r'.*\.gz$', input_filename): cmd = ["zcat", input_filename] elif re.match(r'.*\.bz2$', input_filename): @@ -447,13 +539,19 @@ def open_input_file(input_filename): return input_file -def open_output_file(input_filename): - # create a regex that creates the output filename +def get_output_filename(input_filename, parquet = False): output_filename = re.sub(r'\.(7z|gz|bz2)?$', '', input_filename) output_filename = re.sub(r'\.xml', '', output_filename) - output_filename = output_filename + ".tsv" - output_file = open(output_filename, "w") + if parquet is False: + output_filename = output_filename + ".tsv" + else: + output_filename = output_filename + ".parquet" + return output_filename +def open_output_file(input_filename): + # create a regex that creates the output filename + output_filename = get_output_filename(input_filename, parquet = False) + output_file = open(output_filename, "w") return output_file parser = argparse.ArgumentParser(description='Parse MediaWiki XML database dumps into tab delimitted data.') @@ -463,7 +561,7 @@ parser.add_argument('dumpfiles', metavar="DUMPFILE", nargs="*", type=str, help="Filename of the compressed or uncompressed XML database dump. If absent, we'll look for content on stdin and output on stdout.") parser.add_argument('-o', '--output-dir', metavar='DIR', dest='output_dir', type=str, nargs=1, - help="Directory for output files.") + help="Directory for output files. If it ends with .parquet output will be in parquet format.") parser.add_argument('-s', '--stdout', dest="stdout", action="store_true", help="Write output to standard out (do not create dump file)") @@ -502,6 +600,8 @@ parser.add_argument('-CPl', '--comment-pattern-label', dest="regex_comment_label args = parser.parse_args() + + # set persistence method if args.persist is None: @@ -519,6 +619,7 @@ else: namespaces = None if len(args.dumpfiles) > 0: + output_parquet = False for filename in args.dumpfiles: input_file = open_input_file(filename) @@ -528,13 +629,16 @@ if len(args.dumpfiles) > 0: else: output_dir = "." + if output_dir.endswith(".parquet"): + output_parquet = True + print("Processing file: %s" % filename, file=sys.stderr) if args.stdout: output_file = sys.stdout else: filename = os.path.join(output_dir, os.path.basename(filename)) - output_file = open_output_file(filename) + output_file = get_output_filename(filename, parquet = output_parquet) wikiq = WikiqParser(input_file, output_file, @@ -546,13 +650,15 @@ if len(args.dumpfiles) > 0: regex_match_revision = args.regex_match_revision, regex_revision_label = args.regex_revision_label, regex_match_comment = args.regex_match_comment, - regex_comment_label = args.regex_comment_label) + regex_comment_label = args.regex_comment_label, + output_parquet=output_parquet) + print(wikiq.output_parquet) wikiq.process() # close things input_file.close() - output_file.close() + else: wikiq = WikiqParser(sys.stdin, sys.stdout,