X-Git-Url: https://code.communitydata.science/mediawiki_dump_tools.git/blobdiff_plain/f147e1d899ea269dad715aea393153683353e946..ae9a2417472efb1a13bef2cfe8c86cafe01c5e9d:/wikiq diff --git a/wikiq b/wikiq index 7a1b846..377e95f 100755 --- a/wikiq +++ b/wikiq @@ -8,6 +8,7 @@ import argparse import sys import os, os.path import re +from datetime import datetime from subprocess import Popen, PIPE from collections import deque @@ -24,6 +25,11 @@ 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 + class PersistMethod: none = 0 sequence = 1 @@ -34,55 +40,6 @@ def calculate_persistence(tokens_added): return(sum([(len(x.revisions)-1) for x in tokens_added]), len(tokens_added)) -def matchmake(scanned_content, rev_data, regex, label): - p = re.compile(regex) - - temp_dict = {} - # if there are named capture groups in the regex - if bool(p.groupindex): - capture_groups = list(p.groupindex.keys()) - - # initialize the {capture_group_name:list} for each capture group - for cap_group in capture_groups: - temp_dict["{}_{}".format(label, cap_group)] = [] - - # if there are matches of some sort in this revision content, fill the lists for each cap_group - if p.search(scanned_content) is not None: - m = re.finditer(p,scanned_content) - matchobjects = list(m) - - for cap_group in capture_groups: - temp_list = [] - for match in matchobjects: - # we only want to add the match for the capture group if the match is not None - if match.group(cap_group) != None: - temp_list.append(match.group(cap_group)) - - # if temp_list of matches is empty just make that column None - if len(temp_list)==0: - temp_dict["{}_{}".format(label, cap_group)] = None - # else we put in the list we made in the for-loop above - else: - temp_dict["{}_{}".format(label, cap_group)] = ', '.join(temp_list) - - # there are no matches at all in this revision content, we default values to None - else: - for cap_group in capture_groups: - temp_dict["{}_{}".format(label, cap_group)] = None - - # 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 p.search(scanned_content) is not None: - m = p.findall(scanned_content) - temp_dict[label] = ', '.join(m) - else: - temp_dict[label] = None - # update rev_data with our new columns - rev_data.update(temp_dict) - print(rev_data.keys()) - return rev_data - class WikiqIterator(): def __init__(self, fh, collapse_user=False): @@ -176,31 +133,260 @@ class WikiqPage(): def __next__(self): return next(self.__revisions) + +class RegexPair(object): + def __init__(self, pattern, label): + self.pattern = re.compile(pattern) + self.label = label + self.has_groups = bool(self.pattern.groupindex) + if self.has_groups: + self.capture_groups = list(self.pattern.groupindex.keys()) + + def _make_key(self, cap_group): + return ("{}_{}".format(self.label, cap_group)) + + def matchmake(self, content, rev_data): + + temp_dict = {} + # if there are named capture groups in the regex + if self.has_groups: + + # if there are matches of some sort in this revision content, fill the lists for each cap_group + if self.pattern.search(content) is not None: + m = self.pattern.finditer(content) + matchobjects = list(m) + + for cap_group in self.capture_groups: + key = self._make_key(cap_group) + temp_list = [] + for match in matchobjects: + # we only want to add the match for the capture group if the match is not None + if match.group(cap_group) != None: + temp_list.append(match.group(cap_group)) + + # if temp_list of matches is empty just make that column None + if len(temp_list)==0: + temp_dict[key] = None + # else we put in the list we made in the for-loop above + else: + temp_dict[key] = ', '.join(temp_list) + + # there are no matches at all in this revision content, we default values to None + else: + for cap_group in self.capture_groups: + key = self._make_key(cap_group) + temp_dict[key] = None + + # 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 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 + for k, v in temp_dict: + rev_data.setattr(k,v) + + return rev_data + +@dataclass() +class RevDataBase(): + revid: int + date_time: datetime + articleid: int + editorid: int + title: str + namespace: int + deleted: bool + text_chars: int = None + revert: bool = None + reverteds: list[int] = None + sha1: str = None + minor: bool = None + editor: str = None + anon: bool = None + collapsed_revs:int = None + + pa_schema_fields = [ + pa.field("revid", pa.int64), + pa.field("date_time",pa.timestamp('ms')), + pa.field("articleid",pa.int64()), + pa.field("editorid",pa.int64()), + pa.field("title",pa.string()), + pa.field("namespace",pa.int32()), + pa.field("deleted",pa.binary()), + pa.field("test_chars",pa.int32()), + pa.field("revert",pa.binary()), + pa.field("reverteds",pa.list_(pa.int64())), + pa.field("sha1",pa.string()), + pa.field("minor",pa.binary()), + pa.field("editor",pa.string()), + pa.field("anon",pa.binary()) + ] + + def to_pyarrow(self): + return pa.array(self.astuple(), map(self.pa_schema_fields, pa.field.type)) + + + def to_tsv_row(self): + + row = [] + for f in self.fields(): + val = getattr(self, f.name) + if getattr(self, f.name) is None: + row.append("") + elif f.type == bool: + row.append("TRUE" if val else "FALSE") + + elif f.type == datetime: + row.append(val.strftime('%Y-%m-%d %H:%M:%S')) + + elif f.name in {'editor','title'}: + s = '"' + val + '"' + if f.name in TO_ENCODE: + row.append(quote(str(val))) + + elif f.type == list[int]: + row.append('"' + ",".join([str(x) for x in val]) + '"') + + elif f.type == str: + if f.name in TO_ENCODE: + row.append(quote(str(val))) + else: + row.append(val) + + return '\t'.join(row) + + # def __init__(revid: int, + # date_time: datetime, + # articleid: int, + # editorid: int, + # title: str, + # namespace: int, + # deleted: bool, + # test_chars: int, + # revert: bool, + # reverteds: list[bool], + # sha1: str, + # minor: bool, + # editor: str, + # anon: bool): + + + +@dataclass() +class RevDataCollapse(RevDataBase): + collapsed_revs:int = None + pa_collapsed_revs_schema = pa.field('collapsed_revs',pa.int64()) + pa_schema_fields = RevDataBase.pa_schema_fields + pa_collapsed_revs_schema + pa_schema = pa.schema(pa_schema_fields) + +@dataclass() +class RevDataPersistence(RevDataBase): + token_revs:int = None + tokens_added:int = None + tokens_removed:int = None + tokens_window:int = None + pa_persistence_schema_fields = [ + pa.field(token_revs, pa.int64()), + pa.field(tokens_added, pa.int64()), + pa.field(tokens_removed, pa.int64()), + pa.tokens_window, pa.int64()] + + pa_schema_fields = RevDataBase.pa_schema_fields + pa_persistence_schema_fields + +@dataclass() +class RevDataCollapsePersistence(RevDataCollapse, RevDataPersistence): + pa_scehma_fields = RevDataCollapse.pa_schema_fields + RevDataPersistence.pa_persistence_schema_fields + 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.regex_match_revision = regex_match_revision - self.regex_revision_label = regex_revision_label - self.regex_match_comment = regex_match_comment - self.regex_comment_label = regex_comment_label + + self.output_buffer = [] + self.output_buffer_size = output_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 self.collapse_user is True: + if self.persist == PersistMethod.none: + revdata_type = RevDataCollapse + else: + revdata_type = RevDataCollapsePersistence + elif self.persist != PersistMethod.none: + revdata_type = RevDataPersistence + else: + revdata_type = RevDataBase + + regex_fields = [(field.name, list[str]), for field in self.regex_schemas] + self.revdata_type = dataclasses.make_dataclass('RevData_Parser', + fields=map(regex_fields, + lambda pa_field: (pa_field.name, + list[string], + field(default=None))), + bases=(revdata_type)) + + self.revdata_type.pa_schema_fields = revdata_type.pa_schema_fields + regex_fields + + 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)): + 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: + sys.exit('Each regular expression *must* come with a corresponding label and vice versa.') + + def matchmake(self, rev, rev_data): + rev_data = self.matchmake_revision(rev.text, rev_data) + rev_data = self.matchmake_comment(rev.comment, rev_data) + return rev_data + + def matchmake_revision(self, text, rev_data): + return self.matchmake_pairs(text, rev_data, self.regex_revision_pairs) + + def matchmake_comment(self, comment, rev_data): + return self.matchmake_pairs(comment, rev_data, self.regex_comment_pairs) + + def matchmake_pairs(self, text, rev_data, pairs): + for pair in pairs: + rev_data = pair.matchmake(text, rev_data) + return rev_data + def __get_namespace_from_title(self, title): default_ns = None @@ -243,10 +429,8 @@ class WikiqParser(): if namespace not in self.namespace_filter: continue - print(self.revert_radius) rev_detector = mwreverts.Detector(radius = self.revert_radius) - if self.persist != PersistMethod.none: window = deque(maxlen=PERSISTENCE_RADIUS) @@ -266,60 +450,17 @@ class WikiqParser(): # Iterate through a page's revisions for rev in page: - # initialize rev_data - rev_data = {} + rev_data = self.revdata_type(revid = rev.id, + date_time = rev.timestamp, + articleid = page.id, + editorid = "" if rev.deleted.user == True or rev.user.id is None else rev.user.id, + title = page.title, + deleted = rev.deleted.text + ) - # if the command line args only gave a label (and no regular expression is given) - if (self.regex_revision_label != None and self.regex_match_revision == None) or (self.regex_comment_label != None and self.regex_match_comment == None): - sys.exit('The given regex label(s) has no corresponding regex to search for.') - - # if there's anything in the list of regex_match_revision - if self.regex_match_revision is not None: - if (self.regex_revision_label == None) or (len(self.regex_match_revision) != len(self.regex_revision_label)): - sys.exit('Each regular expression *must* come with a corresponding label and vice versa.') - - # initialize and construct the list of regex-label tuples - pairs = [] - for i in range(0,len(self.regex_match_revision)): - pairs.append((self.regex_match_revision[i], self.regex_revision_label[i])) - - # for each regex/label pair, we now run matchmake to check and output columns - for pair in pairs: - # pair[0] corresponds to the regex, pair[1] to the label - rev_data = matchmake(rev.text, rev_data, pair[0], pair[1]) - - # if there's anything in the list of regex_match_comment - if self.regex_match_comment is not None: - if (self.regex_comment_label == None) or (len(self.regex_match_comment) != len(self.regex_comment_label)): - sys.exit('Each regular expression *must* come with a corresponding label and vice versa.') - - # initialize and construct the list of regex-label tuples - pairs = [] - for i in range(0,len(self.regex_match_comment)): - pairs.append((self.regex_match_comment[i], self.regex_comment_label[i])) - - # for each regex/label pair, we now run matchmake to check and output columns - for pair in pairs: - # pair[0] corresponds to the regex, pair[1] to the label - rev_data = matchmake(rev.comment, rev_data, pair[0], pair[1]) - - # we fill out the rest of the data structure now - rev_data['revid'] = rev.id - rev_data['date_time'] = rev.timestamp.strftime('%Y-%m-%d %H:%M:%S') - rev_data['articleid'] = page.id - rev_data['editor_id'] = "" if rev.deleted.user == True or rev.user.id is None else rev.user.id - rev_data['title'] = '"' + page.title + '"' - rev_data['namespace'] = namespace - rev_data['deleted'] = "TRUE" if rev.deleted.text else "FALSE" - - # if revisions are deleted, /many/ things will be missing - if rev.deleted.text: - rev_data['text_chars'] = "" - rev_data['sha1'] = "" - rev_data['revert'] = "" - rev_data['reverteds'] = "" + rev_data = self.matchmake(rev, rev_data) - else: + if not rev.deleted.text: # rev.text can be None if the page has no text if not rev.text: rev.text = "" @@ -331,33 +472,25 @@ class WikiqParser(): text_sha1 = sha1(bytes(rev.text, "utf8")).hexdigest() - rev_data['sha1'] = text_sha1 + rev_data.sha1 = text_sha1 # TODO rev.bytes doesn't work.. looks like a bug - rev_data['text_chars'] = len(rev.text) + rev_data.text_chars = len(rev.text) # generate revert data - revert = rev_detector.process(text_sha1, rev.id) + rev_data.revert = rev_detector.process(text_sha1, rev.id) if revert: - rev_data['revert'] = "TRUE" - rev_data['reverteds'] = '"' + ",".join([str(x) for x in revert.reverteds]) + '"' - else: - rev_data['revert'] = "FALSE" - rev_data['reverteds'] = "" + rev_data.reverteds = revert.reverteds # if the fact that the edit was minor can be hidden, this might be an issue - rev_data['minor'] = "TRUE" if rev.minor else "FALSE" + rev_data.minor = rev.minor if not rev.deleted.user: # wrap user-defined editors in quotes for fread - rev_data['editor'] = '"' + rev.user.text + '"' - rev_data['anon'] = "TRUE" if rev.user.id == None else "FALSE" + rev_data.editor = rev.user.text + rev_data.anon = rev.user.id == None - else: - rev_data['anon'] = "" - rev_data['editor'] = "" - #if re.match(r'^#redirect \[\[.*\]\]', rev.text, re.I): # redirect = True #else: @@ -367,13 +500,11 @@ class WikiqParser(): # if collapse user was on, lets run that if self.collapse_user: - rev_data['collapsed_revs'] = rev.collapsed_revs + rev_data.collapsed_revs = rev.collapsed_revs if self.persist != PersistMethod.none: - if rev.deleted.text: - for k in ["token_revs", "tokens_added", "tokens_removed", "tokens_window"]: - old_rev_data[k] = None - else: + + if not rev.deleted.text: if self.persist != PersistMethod.legacy: _, tokens_added, tokens_removed = state.update(rev.text, rev.id) @@ -388,12 +519,12 @@ class WikiqParser(): num_token_revs, num_tokens = calculate_persistence(old_tokens_added) - old_rev_data["token_revs"] = num_token_revs - old_rev_data["tokens_added"] = num_tokens - old_rev_data["tokens_removed"] = len(old_tokens_removed) - old_rev_data["tokens_window"] = PERSISTENCE_RADIUS-1 + rev_data.token_revs = num_token_revs + rev_data.tokens_added = num_tokens + rev_data.tokens_removed = len(old_tokens_removed) + rev_data.tokens_window = PERSISTENCE_RADIUS-1 - self.print_rev_data(old_rev_data) + self.print_rev_data(rev_data) else: self.print_rev_data(rev_data) @@ -410,11 +541,10 @@ class WikiqParser(): rev_id, rev_data, tokens_added, tokens_removed = item num_token_revs, num_tokens = calculate_persistence(tokens_added) - rev_data["token_revs"] = num_token_revs - rev_data["tokens_added"] = num_tokens - rev_data["tokens_removed"] = len(tokens_removed) - rev_data["tokens_window"] = len(window)-(i+1) - + rev_data.token_revs = num_token_revs + 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 @@ -422,22 +552,53 @@ 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): + padata = rev_data.to_pyarrow() + self.output_buffer.append(padata) + + if len(self.output_buffer) >= self.output_buffer_size: + self.flush_parquet_buffer() + + + def flush_parquet_buffer(self): + outtable = pa.table.concat_arrays(self.output_buffer) + if self.pq_writer is None: + schema = pa.schema(self.revdata_type.pa_schema_field) + self.pq_writer = pq.ParquetWriter(self.output_file, schema, flavor='spark') + + self.pq_writer.write_table(outtable) + self.output_buffer = [] + def print_rev_data(self, rev_data): - # 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) - self.printed_header = True + if self.output_parquet is False: + printfunc = self.write_tsv_row + else: + printfunc = self.write_parquet_row - print("\t".join([str(v) for k, v in sorted(rev_data.items())]), file=self.output_file) + printfunc(rev_data) + + def write_tsv_row(self, rev_data): + + self.output_buffer.append(rev_data.to_tsv_line()) + + if len(self.output_buffer) >= self.output_buffer_size: + self.flush_tsv_buffer() + def flush_tsv_buffer(): + if self.output_header: + 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$', input_filename): @@ -450,13 +611,19 @@ def open_input_file(input_filename): return input_file -def open_output_file(input_filename): - # create a regex that creates the output filename +def get_output_filename(input_filename, parquet = False): output_filename = re.sub(r'\.(7z|gz|bz2)?$', '', 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.') @@ -466,7 +633,7 @@ 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)") @@ -505,6 +672,8 @@ parser.add_argument('-CPl', '--comment-pattern-label', dest="regex_comment_label args = parser.parse_args() + + # set persistence method if args.persist is None: @@ -522,6 +691,7 @@ else: namespaces = None if len(args.dumpfiles) > 0: + output_parquet = False for filename in args.dumpfiles: input_file = open_input_file(filename) @@ -531,13 +701,16 @@ 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, @@ -549,13 +722,15 @@ 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,