initial work on parquet support

diff --git a/wikiq b/wikiq
index 0543a3383b57ae27281882885bad08978c6de5f9..c2a2f124f7f5b8f86c43a1480fccb4c761043eae 100755 (executable)
--- a/wikiq
+++ b/wikiq
@@ -24,6 +24,13 @@ PERSISTENCE_RADIUS=7
 from deltas import SequenceMatcher
 from deltas import SegmentMatcher
 
 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
 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
         # 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
 
         # 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():
 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
         """ 
         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.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
 
 
         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)
         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)):
 
     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:
         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,
                     '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"
                     '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)
                     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
                     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)
 
         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):
     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:
         # 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
         
             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):
 
 
 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):
     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
 
 
     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)?$', '', input_filename)
     output_filename = re.sub(r'\.xml', '', output_filename)
     output_filename = re.sub(r'\.(7z|gz|bz2)?$', '', 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.')
     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="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)")
 
 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()
 
 
 args = parser.parse_args()
 

+
+

 # set persistence method
 
 if args.persist is None:
 # set persistence method
 
 if args.persist is None:


@@ -519,6 +619,7 @@ else:
     namespaces = None
 
 if len(args.dumpfiles) > 0:
     namespaces = None
 
 if len(args.dumpfiles) > 0:

+    output_parquet = False

     for filename in args.dumpfiles:
         input_file = open_input_file(filename)
 
     for filename in args.dumpfiles:
         input_file = open_input_file(filename)
 


@@ -528,13 +629,16 @@ if len(args.dumpfiles) > 0:
         else:
             output_dir = "."
 
         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))
         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,
 
         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_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()
         wikiq.process()
 
         # close things 
         input_file.close()

-        output_file.close()
+

 else:
     wikiq = WikiqParser(sys.stdin,
                         sys.stdout,
 else:
     wikiq = WikiqParser(sys.stdin,
                         sys.stdout,