sub assertEquals assertEqual

.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 +1,264 @@
+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)
+
+    def test_WP_namespaces(self):
+        print(os.path.abspath('.'))
+        test_filename =  "namespaces_" + 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 + " -n 0 -n 1"
+        print(call)
+        proc = subprocess.Popen(call,stdout=subprocess.PIPE,shell=True)
+        proc.wait()
+        copyfile(self.call_output, test_file)
+        baseline_file = os.path.join(os.path.abspath("."), 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)
+        num_wrong_ns = sum(~ test.namespace.isin({0,1}))
+        self.assertEqual(num_wrong_ns, 0)
+        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_segment(self):
+        test_filename =  "persistence_segment_" + 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 segment"
+        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

@@ -13,12 +13,22 @@ 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
+from deltas import SegmentMatcher
+
+class PersistMethod:
+    none = 0
+    sequence = 1
+    segment = 2
+    legacy = 3
 
 def calculate_persistence(tokens_added):
     return(sum([(len(x.revisions)-1) for x in tokens_added]),
@@ -28,12 +38,16 @@ 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 +60,19 @@ 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
+        # following mwxml, we assume namespace 0 in cases where
+        # page.namespace is inconsistent with namespace_map
+        if page.namespace not in namespace_map:
+            self.title = page.title
+            page.namespace = 0
+        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 +96,14 @@ 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 +116,7 @@ class WikiqPage():
                     yield prev_rev
 
             prev_rev = rev
+
         # also yield the final time
         yield prev_rev
 
@@ -100,8 +128,11 @@ class WikiqPage():
 
 class WikiqParser():
     
-
+    def __init__(self, input_file, output_file, collapse_user=False, persist=None, urlencode=False, namespaces = None):
-    def __init__(self, input_file, output_file, collapse_user=False, persist=False, urlencode=False):
+        """ 
+        Parameters:
+           persist : what persistence method to use. Takes a PersistMethod value
+        """
 
         self.input_file = input_file
         self.output_file = output_file
@@ -110,6 +141,10 @@ class WikiqParser():
         self.printed_header = False
         self.namespaces = []
         self.urlencode = urlencode
+        if namespaces is not None:
+            self.namespace_filter = set(namespaces)
+        else:
+            self.namespace_filter = None
 
     def __get_namespace_from_title(self, title):
         default_ns = None
@@ -137,17 +172,38 @@ 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:
+            namespace = page.namespace if page.namespace is not None else self.__get_namespace_from_title(page.title)
-                state = persistence.State()
+
+            # skip namespaces not in the filter
+            if self.namespace_filter is not None:
+                if namespace not in self.namespace_filter:
+                    continue
+
+            rev_detector = mwreverts.Detector()
+
+            if self.persist != PersistMethod.none:
                 window = deque(maxlen=PERSISTENCE_RADIUS)
 
-            rev_detector = reverts.Detector()
+                if self.persist == PersistMethod.sequence:
+                    state = mwpersistence.DiffState(SequenceMatcher(tokenizer = wikitext_split),
+                                                    revert_radius=PERSISTENCE_RADIUS)
+
+                elif self.persist == PersistMethod.segment:
+                    state = mwpersistence.DiffState(SegmentMatcher(tokenizer = wikitext_split),
+                                                    revert_radius=PERSISTENCE_RADIUS)
+
+                # self.persist == PersistMethod.legacy
+                else:
+                    from mw.lib import persistence
+                    state = persistence.State()
 
             # Iterate through a page's revisions
             for rev in page:
@@ -155,23 +211,28 @@ 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' : namespace,
-                            '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 +242,7 @@ 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 +253,10 @@ 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 +273,18 @@ class WikiqParser():
                 if self.collapse_user:
                     rev_data['collapsed_revs'] = rev.collapsed_revs
 
-                if self.persist:
+                if self.persist != PersistMethod.none:
-                    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:
+
+                        if self.persist != PersistMethod.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 +304,7 @@ class WikiqParser():
 
                 rev_count += 1
 
-            if self.persist:
+            if self.persist != PersistMethod.none:
                 # 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 +345,7 @@ 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
@@ -310,14 +378,35 @@ parser.add_argument('-s', '--stdout', dest="stdout", action="store_true",
 parser.add_argument('--collapse-user', dest="collapse_user", action="store_true",
                     help="Operate only on the final revision made by user a user within all sequences of consecutive edits made by a user. This can be useful for addressing issues with text persistence measures.")
 
-parser.add_argument('-p', '--persistence', dest="persist", action="store_true",
+parser.add_argument('-p', '--persistence', dest="persist", default=None, const='', type=str, choices = ['','segment','sequence','legacy'], nargs='?',
-                    help="Compute and report measures of content persistent: (1) persistent token revisions, (2) tokens added, and (3) number of revision used in computing the first measure.")
+                    help="Compute and report measures of content persistent: (1) persistent token revisions, (2) tokens added, and (3) number of revision used in computing the first measure. This may by slow.  Use -p=segment for advanced persistence calculation method that is robust to content moves. This might be very slow. Use -p=legacy for legacy behavior.")
 
 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('-n', '--namespace-include', dest="namespace_filter", type=int, action='append',
+                    help="Id number of namspace to include.")
+
+
+
 args = parser.parse_args()
 
+# set persistence method
+
+if args.persist is None:
+    persist = PersistMethod.none
+elif args.persist == "segment":
+    persist = PersistMethod.segment
+elif args.persist == "legacy":
+    persist = PersistMethod.legacy
+else:
+    persist = PersistMethod.sequence
+
+if args.namespace_filter is not None:
+    namespaces = args.namespace_filter
+else:
+    namespaces = None
+
 if len(args.dumpfiles) > 0:
     for filename in args.dumpfiles:
         input_file = open_input_file(filename)
@@ -338,9 +427,9 @@ if len(args.dumpfiles) > 0:
 
         wikiq = WikiqParser(input_file, output_file, 
                             collapse_user=args.collapse_user,
-                            persist=args.persist,
+                            persist=persist,
-                            urlencode=args.urlencode)
+                            urlencode=args.urlencode,
-
+                            namespaces = namespaces)
 
         wikiq.process()
 
@@ -350,8 +439,10 @@ if len(args.dumpfiles) > 0:
 else:
     wikiq = WikiqParser(sys.stdin, sys.stdout,
                         collapse_user=args.collapse_user,
-                        persist=args.persist,
+                        persist=persist,
-                        urlencode=args.urlencode)
+                        persist_legacy=args.persist_legacy,
+                        urlencode=args.urlencode,
+                        namespaces = namespaces)
     wikiq.process()
 
 # stop_words = "a,able,about,across,after,all,almost,also,am,among,an,and,any,are,as,at,be,because,been,but,by,can,cannot,could,dear,did,do,does,either,else,ever,every,for,from,get,got,had,has,have,he,her,hers,him,his,how,however,i,if,in,into,is,it,its,just,least,let,like,likely,may,me,might,most,must,my,neither,no,nor,not,of,off,often,on,only,or,other,our,own,rather,said,say,says,she,should,since,so,some,than,that,the,their,them,then,there,these,they,this,tis,to,too,twas,us,wants,was,we,were,what,when,where,which,while,who,whom,why,will,with,would,yet,you,your"