Prefix page titles with namespace names.

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "Mediawiki-Utilities"]
-	path = Mediawiki-Utilities
-	url = https://github.com/halfak/Mediawiki-Utilities.git

README.rst

@@ -7,3 +7,7 @@ submodule like::
 
   git submodule init
   git submodule update
+
+
+Wikimedia dumps are usually in a compressed format such as 7z (most common), gz, or bz2. Wikiq uses your computer's compression software to read these files. Therefore wikiq depends on
+`7za`, `gzcat`, and `zcat`. 

mw

@@ -1 +0,0 @@
-Mediawiki-Utilities/mw

test/Wikiq_Unit_Test.py

@@ -0,0 +1,223 @@
+import unittest
+import os
+import subprocess
+from shutil import copyfile
+import pandas as pd
+from pandas.util.testing import assert_frame_equal
+from io import StringIO
+
+# with / without pwr DONE
+# with / without url encode DONE
+# with / without collapse user DONE
+# with output to sdtout DONE
+# note that the persistence radius is 7 by default
+# reading various file formats including
+#        7z, gz, bz2, xml  DONE
+# wikia and wikipedia data DONE
+# malformed xmls DONE
+
+class Test_Wikipedia(unittest.TestCase):
+    def setUp(self):
+        if not os.path.exists("test_output"):
+            os.mkdir("test_output")
+
+        self.wiki = 'ikwiki-20180301-pages-meta-history'
+        self.wikiq_out_name =  self.wiki + ".tsv"
+        self.test_output_dir = os.path.join(".", "test_output")
+        self.call_output = os.path.join(self.test_output_dir, self.wikiq_out_name)
+
+        self.infile = "{0}.xml.bz2".format(self.wiki)    
+        self.base_call = "../wikiq {0} -o {1}"
+        self.input_dir = "dumps"
+        self.input_file = os.path.join(".", self.input_dir,self.infile)
+        self.baseline_output_dir = "baseline_output"
+
+    def test_WP_url_encode(self):
+        test_filename =  "url-encode_" + self.wikiq_out_name
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        call = call + " --url-encode"
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+        copyfile(self.call_output, test_file)
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+
+        # as a test let's make sure that we get equal data frames
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+
+class Test_Basic(unittest.TestCase):
+
+    def setUp(self):
+        if not os.path.exists("test_output"):
+            os.mkdir("test_output")
+
+        self.wiki = 'sailormoon'
+        self.wikiq_out_name =  self.wiki + ".tsv"
+        self.test_output_dir = os.path.join(".", "test_output")
+        self.call_output = os.path.join(self.test_output_dir, self.wikiq_out_name)
+
+        self.infile = "{0}.xml.7z".format(self.wiki)
+        self.base_call = "../wikiq {0} -o {1}"
+        self.input_dir = "dumps"
+        self.input_file = os.path.join(".", self.input_dir,self.infile)
+        self.baseline_output_dir = "baseline_output"
+
+    def test_noargs(self):
+
+        test_filename =  "noargs_" + self.wikiq_out_name
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+        copyfile(self.call_output, test_file)
+
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+
+    def test_collapse_user(self):
+        test_filename =  "collapse-user_" + self.wikiq_out_name
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        call = call + " --collapse-user"
+
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+        copyfile(self.call_output, test_file)
+
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+    def test_pwr_legacy(self):
+        test_filename =  "persistence_legacy_" + self.wikiq_out_name
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        call = call + " --persistence-legacy"
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+
+        copyfile(self.call_output, test_file)
+
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+    def test_pwr(self):
+        test_filename =  "persistence_" + self.wikiq_out_name
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        call = call + " --persistence"
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+
+        copyfile(self.call_output, test_file)
+
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+
+    def test_url_encode(self):
+        test_filename =  "url-encode_" + self.wikiq_out_name
+
+        test_file = os.path.join(self.test_output_dir, test_filename)
+        if os.path.exists(test_file):
+            os.remove(test_file)
+        
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        call = call + " --url-encode"
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+
+        copyfile(self.call_output, test_file)
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_filename)
+        test = pd.read_table(test_file)
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+
+
+class Test_Malformed(unittest.TestCase):
+
+    def setUp(self):
+        if not os.path.exists("test_output"):
+            os.mkdir("test_output")
+
+        self.wiki = 'twinpeaks'
+        self.wikiq_out_name =  self.wiki + ".tsv"
+        self.test_output_dir = os.path.join(".", "test_output")
+        self.call_output = os.path.join(self.test_output_dir, self.wikiq_out_name)
+
+        self.infile = "{0}.xml.7z".format(self.wiki)
+        self.base_call = "../wikiq {0} -o {1}"
+        self.input_dir = "dumps"
+        self.input_file = os.path.join(".", self.input_dir,self.infile)
+
+
+    def test_malformed_noargs(self):
+
+        call = self.base_call.format(self.input_file, self.test_output_dir)
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,stderr=subprocess.PIPE, shell=True)
+        proc.wait()
+        outs, errs = proc.communicate()
+        errlines = str(errs).split("\\n")
+        self.assertEqual(errlines[-2],'xml.etree.ElementTree.ParseError: no element found: line 1369, column 0')
+
+class Test_Stdout(unittest.TestCase):
+
+    def setUp(self):
+        self.wiki = 'sailormoon'
+        self.wikiq_out_name =  self.wiki + ".tsv"
+
+        self.infile = "{0}.xml.7z".format(self.wiki)
+        self.base_call = "../wikiq {0} --stdout"
+        self.input_dir = "dumps"
+        self.input_file = os.path.join(".", self.input_dir,self.infile)
+        self.baseline_output_dir = "baseline_output"
+
+    def test_noargs(self):
+
+        call = self.base_call.format(self.input_file)
+        proc = subprocess.run(call,stdout=subprocess.PIPE,shell=True)
+        outs = proc.stdout.decode("utf8")
+
+        test_file = "noargs_" + self.wikiq_out_name
+        baseline_file = os.path.join(".", self.baseline_output_dir, test_file)
+        print(baseline_file)
+        test = pd.read_table(StringIO(outs))
+        baseline = pd.read_table(baseline_file)
+        assert_frame_equal(test,baseline)
+        
+if __name__ == '__main__':
+    unittest.main()

wikiq

@@ -3,7 +3,7 @@
 # original wikiq headers are: title articleid revid date_time anon
 # editor editor_id minor text_size text_entropy text_md5 reversion
 # additions_size deletions_size
-
+import pdb
 import argparse
 import sys
 import os, os.path
@@ -13,27 +13,35 @@ from subprocess import Popen, PIPE
 from collections import deque
 from hashlib import sha1
 
-from mw.xml_dump import Iterator
+from mwxml import Dump
-from mw.lib import persistence
+
-from mw.lib import reverts
+from deltas.tokenizers import wikitext_split
+import mwpersistence
+import mwreverts
 from urllib.parse import quote
 TO_ENCODE = ('title', 'editor')
 PERSISTENCE_RADIUS=7
+from deltas import SequenceMatcher
 
 def calculate_persistence(tokens_added):
     return(sum([(len(x.revisions)-1) for x in tokens_added]),
            len(tokens_added))
 
+
 class WikiqIterator():
     def __init__(self, fh, collapse_user=False):
         self.fh = fh
         self.collapse_user = collapse_user
-        self.mwiterator = Iterator.from_file(self.fh)
+        self.mwiterator = Dump.from_file(self.fh)
+        self.namespace_map = { ns.id : ns.name for ns in
+                               self.mwiterator.site_info.namespaces }
         self.__pages = self.load_pages()
 
     def load_pages(self):
         for page in self.mwiterator:
-            yield WikiqPage(page, collapse_user=self.collapse_user)
+            yield WikiqPage(page,
+                            namespace_map = self.namespace_map,
+                            collapse_user=self.collapse_user)
 
     def __iter__(self):
         return self.__pages
@@ -46,13 +54,14 @@ class WikiqPage():
                  'restrictions', 'mwpage', '__revisions',
                  'collapse_user')
     
-    def __init__(self, page, collapse_user=False):
+    def __init__(self, page, namespace_map, collapse_user=False):
         self.id = page.id
-        self.title = page.title
         self.namespace = page.namespace
-        self.redirect = page.redirect
+        if page.namespace != 0:
+            self.title = ':'.join([namespace_map[page.namespace], page.title])
+        else:
+            self.title = page.title
         self.restrictions = page.restrictions
-        
         self.collapse_user = collapse_user
         self.mwpage = page
         self.__revisions = self.rev_list()
@@ -76,7 +85,14 @@ class WikiqPage():
             else:
                 if self.collapse_user:
                     # yield if this is the last edit in a seq by a user and reset
-                    if not rev.contributor.user_text == prev_rev.contributor.user_text:
+                    # also yield if we do know who the user is
+
+                    if rev.deleted.user or prev_rev.deleted.user:
+                        yield prev_rev
+                        collapsed_revs = 1
+                        rev.collapsed_revs = collapsed_revs
+
+                    elif not rev.user.text == prev_rev.user.text:
                         yield prev_rev
                         collapsed_revs = 1
                         rev.collapsed_revs = collapsed_revs
@@ -89,6 +105,7 @@ class WikiqPage():
                     yield prev_rev
 
             prev_rev = rev
+
         # also yield the final time
         yield prev_rev
 
@@ -100,13 +117,13 @@ class WikiqPage():
 
 class WikiqParser():
 
-
+    def __init__(self, input_file, output_file, collapse_user=False, persist=False, urlencode=False, persist_legacy=False):
-    def __init__(self, input_file, output_file, collapse_user=False, persist=False, urlencode=False):
         
         self.input_file = input_file
         self.output_file = output_file
         self.collapse_user = collapse_user
         self.persist = persist
+        self.persist_legacy = persist_legacy
         self.printed_header = False
         self.namespaces = []
         self.urlencode = urlencode
@@ -137,17 +154,26 @@ class WikiqParser():
         dump = WikiqIterator(self.input_file, collapse_user=self.collapse_user)
 
         # extract list of namspaces
-        self.namespaces = {ns.name : ns.id for ns in dump.mwiterator.namespaces}
+        self.namespaces = {ns.name : ns.id for ns in dump.mwiterator.site_info.namespaces}
 
         page_count = 0
         rev_count = 0
+
+
         # Iterate through pages
         for page in dump:
-            if self.persist:
+            rev_detector = mwreverts.Detector()
-                state = persistence.State()
+
+            if self.persist or self.persist_legacy:
                 window = deque(maxlen=PERSISTENCE_RADIUS)
 
-            rev_detector = reverts.Detector()
+                if not self.persist_legacy:
+                    state = mwpersistence.DiffState(SequenceMatcher(tokenizer = wikitext_split),
+                                                    revert_radius=PERSISTENCE_RADIUS)
+
+                else:
+                    from mw.lib import persistence
+                    state = persistence.State()
 
             # Iterate through a page's revisions
             for rev in page:
@@ -155,23 +181,28 @@ class WikiqParser():
                 rev_data = {'revid' : rev.id,
                             'date_time' : rev.timestamp.strftime('%Y-%m-%d %H:%M:%S'),
                             'articleid' : page.id,
-                            'editor_id' : "" if rev.contributor.id == None else rev.contributor.id,
+                            'editor_id' : "" if rev.deleted.user == True or rev.user.id is None else rev.user.id,
                             'title' : '"' + page.title + '"',
-                            'namespace' : page.namespace if page.namespace else self.__get_namespace_from_title(page.title),
+                            'namespace' : page.namespace if page.namespace is not None else self.__get_namespace_from_title(page.title),
-                            'deleted' : "TRUE" if rev.text.deleted else "FALSE" } 
+                            'deleted' : "TRUE" if rev.deleted.text else "FALSE" } 
 
                 # if revisions are deleted, /many/ things will be missing
-                if rev.text.deleted:
+                if rev.deleted.text:
                     rev_data['text_chars'] = ""
                     rev_data['sha1'] = ""
                     rev_data['revert'] = ""
                     rev_data['reverteds'] = ""
 
                 else:
+                    # rev.text can be None if the page has no text
+                    if not rev.text:
+                        rev.text = ""
                     # if text exists, we'll check for a sha1 and generate one otherwise
+
                     if rev.sha1:
                         text_sha1 = rev.sha1
                     else:
+
                         text_sha1 = sha1(bytes(rev.text, "utf8")).hexdigest()
                     
                     rev_data['sha1'] = text_sha1
@@ -181,6 +212,7 @@ class WikiqParser():
                
                     # generate revert 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]) + '"'
@@ -191,10 +223,10 @@ class WikiqParser():
                 # 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"
 
-                if rev.contributor.user_text:
+                if not rev.deleted.user:
                     # wrap user-defined editors in quotes for fread
-                    rev_data['editor'] = '"' + rev.contributor.user_text + '"'
+                    rev_data['editor'] = '"' + rev.user.text + '"'
-                    rev_data['anon'] = "TRUE" if rev.contributor.id == None else "FALSE"
+                    rev_data['anon'] = "TRUE" if rev.user.id == None else "FALSE"
                     
                 else:
                     rev_data['anon'] = ""
@@ -211,12 +243,19 @@ class WikiqParser():
                 if self.collapse_user:
                     rev_data['collapsed_revs'] = rev.collapsed_revs
 
-                if self.persist:
+                if self.persist or self.persist_legacy:
-                    if rev.text.deleted:
+                    if rev.deleted.text:
+
                         for k in ["token_revs", "tokens_added", "tokens_removed", "tokens_window"]:
                             old_rev_data[k] = None
                     else:
-                        _, tokens_added, tokens_removed = state.process(rev.text, rev.id, text_sha1)
+
+                        if not self.persist_legacy:
+                            _, tokens_added, tokens_removed = state.update(rev.text, rev.id)
+
+                        else:
+                            _, tokens_added, tokens_removed = state.process(rev.text, rev.id, text_sha1)
+                            
                         window.append((rev.id, rev_data, tokens_added, tokens_removed))
                         
                         if len(window) == PERSISTENCE_RADIUS:
@@ -236,7 +275,7 @@ class WikiqParser():
 
                 rev_count += 1
 
-            if self.persist:
+            if self.persist or self.persist_legacy:
                 # print out metadata for the last RADIUS revisions
                 for i, item in enumerate(window):
                     # if the window was full, we've already printed item 0
@@ -277,7 +316,7 @@ def open_input_file(input_filename):
     elif re.match(r'.*\.gz$', input_filename):
         cmd = ["zcat", input_filename] 
     elif re.match(r'.*\.bz2$', input_filename):
-        cmd = ["zcat", input_filename] 
+        cmd = ["bzcat", "-dk", input_filename] 
 
     try:
         input_file = Popen(cmd, stdout=PIPE).stdout
@@ -316,6 +355,9 @@ parser.add_argument('-p', '--persistence', dest="persist", action="store_true",
 parser.add_argument('-u', '--url-encode', dest="urlencode", action="store_true",
                     help="Output url encoded text strings. This works around some data issues like newlines in editor names. In the future it may be used to output other text data.")
 
+parser.add_argument('--persistence-legacy', dest="persist_legacy", action="store_true",
+                    help="Legacy behavior for persistence calculation. Output url encoded text strings. This works around some data issues like newlines in editor names. In the future it may be used to output other text data.")
+
 args = parser.parse_args()
 
 if len(args.dumpfiles) > 0:
@@ -339,6 +381,7 @@ if len(args.dumpfiles) > 0:
         wikiq = WikiqParser(input_file, output_file, 
                             collapse_user=args.collapse_user,
                             persist=args.persist,
+                            persist_legacy=args.persist_legacy,
                             urlencode=args.urlencode)
 
 
@@ -351,6 +394,7 @@ else:
     wikiq = WikiqParser(sys.stdin, sys.stdout,
                         collapse_user=args.collapse_user,
                         persist=args.persist,
+                        persist_legacy=args.persist_legacy,
                         urlencode=args.urlencode)
     wikiq.process()