diff options
| -rw-r--r-- | .gitignore | 4 | ||||
| -rw-r--r-- | Makefile | 6 | ||||
| -rw-r--r-- | Pipfile | 1 | ||||
| -rw-r--r-- | fuzzycat/__main__.py | 37 | ||||
| -rw-r--r-- | fuzzycat/cluster.py | 208 | ||||
| -rw-r--r-- | fuzzycat/sandcrawler-title-denylist.txt | 559 |
6 files changed, 761 insertions, 54 deletions
@@ -133,3 +133,7 @@ dmypy.json /names.db /tmp fixtures/cluster_title_normalized_dups_size_keylen.tsv + +# Text Editors +*~ +*.swp @@ -16,7 +16,7 @@ deps: ## Install dependencies from setup.py into pipenv pipenv install --pre '-e .[dev]' .PHONY: style -style: ## Apply import sorting and black source formatting on all files +style: ## Apply import sorting and yapf source formatting on all files isort --atomic fuzzycat/* yapf -p -i -r fuzzycat/* yapf -p -i -r tests @@ -27,11 +27,11 @@ dist: ## Create source distribution and wheel .PHONY: cov cov: ## Run coverage report - pytest --cov=fuzzycat tests/ + pytest --cov=fuzzycat fuzzycat/*.py tests/ .PHONY: test test: ## Run coverage report - pytest -v tests/ + pytest -v fuzzycat/*.py tests/ .PHONY: lint lint: $(PY_FILES) @@ -20,6 +20,7 @@ importlib-metadata = "==1.7.0" tokenizers = "*" spacy = "*" nltk = "*" +regex = "*" [requires] python_version = "3.7" diff --git a/fuzzycat/__main__.py b/fuzzycat/__main__.py index 3845245..a65eb63 100644 --- a/fuzzycat/__main__.py +++ b/fuzzycat/__main__.py @@ -20,9 +20,9 @@ import pstats import sys import tempfile -from fuzzycat.build import NgramLookup, TitleTokenList from fuzzycat.cluster import (Cluster, release_key_title, release_key_title_ngram, - release_key_title_normalized, release_key_title_nysiis) + release_key_title_normalized, release_key_title_nysiis, + release_key_title_sandcrawler) def run_cluster(args): @@ -32,10 +32,16 @@ def run_cluster(args): 'tnorm': release_key_title_normalized, 'tnysi': release_key_title_nysiis, 'tss': release_key_title_ngram, + 'tsandcrawler': release_key_title_sandcrawler, } + key_denylist = None + if args.key_denylist: + with open(args.key_denylist, 'r') as f: + key_denylist = [l.strip() for l in f.readlines()] cluster = Cluster(iterable=fileinput.input(args.files), key=types.get(args.type), tmpdir=args.tmpdir, + key_denylist=key_denylist, prefix=args.prefix) stats = cluster.run() logger.debug(json.dumps(dict(stats))) @@ -49,20 +55,6 @@ def run_verify(args): pass -def run_build(args): - """ - Trying out. - """ - if args.type == "ss": - builder = NgramLookup(files=args.files, output=args.output) - builder.run() - elif args.type == "tt": - builder = TitleTokenList(files=args.files, output=args.output) - builder.run() - else: - raise NotImplementedError() - - if __name__ == '__main__': logging.basicConfig( level=logging.DEBUG, @@ -82,25 +74,16 @@ if __name__ == '__main__': sub_cluster = subparsers.add_parser('cluster', help='group entities', parents=[parser]) sub_cluster.set_defaults(func=run_cluster) sub_cluster.add_argument('-f', '--files', default="-", help='input files') + sub_cluster.add_argument('--key-denylist', help='file path to key denylist') sub_cluster.add_argument('-t', '--type', default='title', - help='cluster algorithm: title, tnorm, tnysi, tss') + help='cluster algorithm: title, tnorm, tnysi, tss, tsandcrawler') sub_verify = subparsers.add_parser('verify', help='verify groups', parents=[parser]) sub_verify.add_argument('-f', '--files', default="-", help='input files') sub_verify.set_defaults(func=run_verify) - sub_build = subparsers.add_parser('build', help='build auxiliary databases', parents=[parser]) - sub_build.add_argument('-f', '--files', default="-", help='input files') - sub_build.add_argument('-t', '--type', default="ss", help='type of database to build') - sub_build.add_argument('-o', - '--output', - type=argparse.FileType('w'), - default=sys.stdout, - help='output file') - sub_build.set_defaults(func=run_build) - args = parser.parse_args() if not args.__dict__.get("func"): print(__doc__, file=sys.stderr) diff --git a/fuzzycat/cluster.py b/fuzzycat/cluster.py index 97509e7..87b010e 100644 --- a/fuzzycat/cluster.py +++ b/fuzzycat/cluster.py @@ -69,15 +69,18 @@ import string import subprocess import sys import tempfile +import unicodedata from dataclasses import dataclass, field from typing import IO, Any, Callable, Dict, Generator, List, Optional, Tuple import fuzzy +import regex __all__ = [ "release_key_title", "release_key_title_normalized", "release_key_title_nysiis", + "release_key_title_sandcrawler", "sort_by_column", "group_by", "Cluster", @@ -157,6 +160,159 @@ def release_key_title_nysiis(doc: KeyDoc) -> Tuple[str, str]: return (ident, fuzzy.nysiis(title)) +# from http://zderadicka.eu/removing-diacritics-marks-from-strings/ +SANDCRAWLER_CHAR_MAP = { + '\N{Latin capital letter AE}': 'AE', + '\N{Latin small letter ae}': 'ae', + '\N{Latin capital letter Eth}': 'D', + '\N{Latin small letter eth}': 'd', + '\N{Latin capital letter O with stroke}': 'O', + '\N{Latin small letter o with stroke}': 'o', + '\N{Latin capital letter Thorn}': 'Th', + '\N{Latin small letter thorn}': 'th', + '\N{Latin small letter sharp s}': 's', + '\N{Latin capital letter D with stroke}': 'D', + '\N{Latin small letter d with stroke}': 'd', + '\N{Latin capital letter H with stroke}': 'H', + '\N{Latin small letter h with stroke}': 'h', + '\N{Latin small letter dotless i}': 'i', + '\N{Latin small letter kra}': 'k', + '\N{Latin capital letter L with stroke}': 'L', + '\N{Latin small letter l with stroke}': 'l', + '\N{Latin capital letter Eng}': 'N', + '\N{Latin small letter eng}': 'n', + '\N{Latin capital ligature OE}': 'Oe', + '\N{Latin small ligature oe}': 'oe', + '\N{Latin capital letter T with stroke}': 'T', + '\N{Latin small letter t with stroke}': 't', + + # bnewbold additions + '\N{MICRO SIGN}': 'u', + '\N{LATIN SMALL LETTER C}': 'c', + '\N{LATIN SMALL LETTER F WITH HOOK}': 'f', + # bnewbold map-to-null (for non-printing stuff not in the regex) + '\N{PARTIAL DIFFERENTIAL}': '', + '\N{LATIN LETTER INVERTED GLOTTAL STOP}': '', + '\N{N-ARY SUMMATION}': '', + '\N{N-ARY PRODUCT}': '', + '\N{MODIFIER LETTER CIRCUMFLEX ACCENT}': '', + '\N{SNOWMAN}': '', + '\N{CARON}': '', +} + +SANDCRAWLER_PREFIX_REMOVE = [ + "original article: ", + "original article ", + "article: ", + "title: ", +] + +# regex that matches all characters which should be removed +SANDCRAWLER_REMOVE_CHAR_REGEX = regex.compile( + r"[\s\p{Punctuation}\p{M}\p{InCombiningDiacriticalMarks}\u2000-\u206F\u2E00-\u2E7F’·“”‘’“”«»「」¿–±§_`°ʖ©®¤=<>|+$^~≈√∫≤≥÷ƒ∆¬£¢∞¥◊€]" +) + + +def sandcrawler_slugify(raw: str) -> str: + """ + Python re-implementation of sandcrawler Scala code for string comparison + ("scorable" strings) + """ + slug = raw.strip().lower() + + # transforms before running regex + for prefix in SANDCRAWLER_PREFIX_REMOVE: + if slug.startswith(prefix): + slug = slug[:len(prefix)] + + slug = slug.replace("'", "'") + + # iterate over all chars and replace from map, if in map; then lower-case again + slug = ''.join([SANDCRAWLER_CHAR_MAP.get(c, c) for c in slug]) + + # early bailout before executing regex + if not slug: + return "" + + slug = unicodedata.normalize('NFKD', slug) + slug = SANDCRAWLER_REMOVE_CHAR_REGEX.sub('', slug) + + return slug.lower() + + +def test_sandcrawler_slugify() -> None: + test_cases = [ + ("", ""), + ("asdf", "asdf"), + ("'Hello World!'", "helloworld"), + ("ASDF", "asdf"), + ("as\n df", "asdf"), + ("as\u0142 bb \u00f8", "aslbbo"), + ("`hello¿", "hello"), + ("علمية", "علمية"), + ("期刊的数字", "期刊的数字"), + ("les pré-impressions explorées à partir", "lespreimpressionsexploreesapartir"), + + # "MICRO SIGN" + ("\xb5meter", "umeter"), + # "GREEK SMALL LETTER MU" + ("\u03bcmeter", "\u03bcmeter"), + + # TODO: ("salt ∧ pepper", "saltpepper"), + # TODO: ("new <b>and</b> improved", "newandimproved"), + + # some via https://github.com/minimaxir/big-list-of-naughty-strings/blob/master/blns.txt + ("-9223372036854775808/-1", "92233720368547758081"), + (r",./;'[]\-= <>?:\"{}|_+ !@#$%^&*()`~", ""), + (" \n\r \x85 \u1680\u2002\u2003\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200a\u200b\u202f\u205f\u3000", + ""), + (r"Ω≈ç√∫˜≤≥÷", "ωc"), + (r"åß∂ƒ©˙∆˚¬…æ", "asfae"), + (r"œ∑´®†¥¨ˆøπ“‘", "oeoπ"), + (r"¡™£¢∞§¶•ªº–≠ ", "tmao"), + (r"¸˛Ç◊ı˜Â¯˘¿", "cia"), + (r"ÅÍÎÏ˝ÓÔÒÚÆ☃", "aiiiooouae"), + (r"Œ„´‰ˇÁ¨ˆØ∏”’", "oeao"), + (r"`⁄€‹›fifl‡°·‚—±", "fifl"), + (r"ЁЂЃЄЅІЇЈЉЊЋЌЍЎЏАБВГДЕЖЗИЙКЛМНОПРСТУФХЦЧШЩЪЫЬЭЮЯабвгдежзийклмнопрстуфхцчшщъыьэюя", + "еђгєѕііјљњћкиуџабвгдежзииклмнопрстуфхцчшщъыьэюяабвгдежзииклмнопрстуфхцчшщъыьэюя"), + (r"⁰⁴⁵₀₁₂", "045012"), + (r"社會科學院語學研究所", "社會科學院語學研究所"), + # TODO: ("パーティーへ行かないか", "パーティーへ行かないか"), + # TODO: ("表ポあA鷗ŒéＢ逍Üߪąñ丂㐀𠀀", "表ポあa鷗oeebＢ逍usaan丂㐀𠀀"), + (r"( ͡° ͜ʖ ͡°)", ""), + # emoji ok? I guess + (r"👾 🙇 💁 🙅 🙆 🙋 🙎 🙍", "👾🙇💁🙅🙆🙋🙎🙍"), + (r"2️⃣ 3️⃣ 4️⃣ 5️⃣", "2345"), + (r"﷽ ", "﷽"), + (r"̗̺͖̹̯͓Ṯ̤͍̥͇͈h̲́e͏͓̼̗̙̼̣͔ ͇̜̱̠͓͍ͅN͕͠e̗̱z̘̝̜̺͙p̤̺̹͍̯͚e̠̻̠͜r̨̤͍̺̖͔̖̖d̠̟̭̬̝͟i̦͖̩͓͔̤a̠̗̬͉̙n͚͜ ̻̞̰͚ͅh̵͉i̳̞v̢͇ḙ͎͟-҉̭̩̼͔m̤̭̫i͕͇̝̦n̗͙ḍ̟ ̯̲͕͞ǫ̟̯̰̲͙̻̝f ̪̰̰̗̖̭̘͘c̦͍̲̞͍̩̙ḥ͚a̮͎̟̙͜ơ̩̹͎s̤.̝̝ ҉Z̡̖̜͖̰̣͉̜a͖̰͙̬͡l̲̫̳͍̩g̡̟̼̱͚̞̬ͅo̗͜.̟", + "thenezperdianhivemindofchaoszalgo"), + (r"Ｔｈｅ ｑｕｉｃｋ ｂｒｏｗｎ ｆｏｘ ｊｕｍｐｓ ｏｖｅｒ ｔｈｅ ｌａｚｙ ｄｏｇ", "thequickbrownfoxjumpsoverthelazydog"), + (r"Ｔｈｅ ｑｕｉｃｋ ｂｒｏｗｎ ｆｏｘ ｊｕｍｐｓ ｏｖｅｒ ｔｈｅ ｌａｚｙ ｄｏｇ", "thequickbrownfoxjumpsoverthelazydog"), + (r"𝕋𝕙𝕖 𝕢𝕦𝕚𝕔𝕜 𝕓𝕣𝕠𝕨𝕟 𝕗𝕠𝕩 𝕛𝕦𝕞𝕡𝕤 𝕠𝕧𝕖𝕣 𝕥𝕙𝕖 𝕝𝕒𝕫𝕪 𝕕𝕠𝕘 ", "thequickbrownfoxjumpsoverthelazydog"), + ] + + for in_str, out_str in test_cases: + if sandcrawler_slugify(in_str) != out_str: + for c in list(sandcrawler_slugify(in_str)): + try: + print(unicodedata.name(c)) + except ValueError: + print(ord(c)) + #print(ord(c)) + print("----") + for c in list(out_str): + print(unicodedata.name(c)) + print(in_str) + assert sandcrawler_slugify(in_str) == out_str + + +def release_key_title_sandcrawler(doc: KeyDoc) -> Tuple[str, str]: + ident, title = release_key_title(doc) + slug = sandcrawler_slugify(title) + return (ident, slug) + + def release_key_title_ngram(doc: KeyDoc, n=3) -> Tuple[str, str]: """ Derive a key from title. @@ -198,22 +354,24 @@ class Cluster: iterable: collections.abc.Iterable, key: Callable[[Any], Tuple[str, str]], output: IO[str] = sys.stdout, + key_denylist: Optional[List[str]] = None, prefix: str = "fuzzycat-", tmpdir: str = tempfile.gettempdir(), strict: bool = False): - """ - Setup a clusterer, using a custom key function. - """ self.iterable: collections.abc.Iterable = iterable self.key: Callable[[Any], Tuple[str, str]] = key self.output: IO[str] = output self.prefix: str = prefix self.tmpdir: str = tmpdir self.counter: Dict[str, int] = collections.Counter({ - "key_err": 0, + "key_fail": 0, "key_ok": 0, + "key_empty": 0, + "key_denylist": 0, "num_clusters": 0, }) + self.strict = strict + self.key_denylist = key_denylist def run(self): """ @@ -226,29 +384,31 @@ class Cluster: try: doc = json.loads(line) id, key = self.key(doc) - # XXX: if the line itself contains tabs, we need to remove - # them here; maybe offer TSV and JSON output and extra flag - print("{}\t{}\t{}".format(id, key, line.replace("\t", " ")), file=tf) except (KeyError, ValueError): if strict: raise - self.counter["key_err"] += 1 - else: - self.counter["key_ok"] += 1 - - try: - sf = self.sort(tf.name, opts='-k 2') - with open(sf) as f: - for doc in self.group_by(f, key=cut(f=1)): - self.counter["num_clusters"] += 1 - json.dump(doc, self.output) - self.output.write("\n") - except Exception as exc: - raise - finally: - os.remove(sf) - os.remove(tf.name) - + self.counter["key_fail"] += 1 + continue + if not key: + self.counter["key_empty"] += 1 + continue + if self.key_denylist and key in self.key_denylist: + self.counter["key_denylist"] += 1 + continue + self.counter["key_ok"] += 1 + # XXX: if the line itself contains tabs, we need to remove + # them here; maybe offer TSV and JSON output and extra flag + print("{}\t{}\t{}".format(id, key, line.replace("\t", " ")), file=tf) + + sf = self.sort(tf.name, opts='-k 2') + with open(sf) as f: + for doc in self.group_by(f, key=cut(f=1)): + self.counter["num_clusters"] += 1 + json.dump(doc, self.output) + self.output.write("\n") + + os.remove(sf) + os.remove(tf.name) return self.counter def sort(self, filename: str, opts: str = "-k 2", fast: bool = True, mode: str = "w"): diff --git a/fuzzycat/sandcrawler-title-denylist.txt b/fuzzycat/sandcrawler-title-denylist.txt new file mode 100644 index 0000000..ef575b4 --- /dev/null +++ b/fuzzycat/sandcrawler-title-denylist.txt @@ -0,0 +1,559 @@ +abbreviations +abbreviationsandacronyms +aboutauthors +abouttheauthor +abouttheauthors +aboutthecover +abouttheeditors +abreviations +abstract +abstractnotsubmittedforonlinepublication +abstractoriginalarticle +abstracts +abstractsofaapaposterandpodiumpresentations +abstractsofcommunications +abstractsofthesesfromthescandinaviancountries +abstractwithdrawn +acknowledgement +acknowledgements +acknowledgementsvii +acknowledgementtoreferees +acknowledgementtoreviewers +acknowledgment +acknowledgmentofreferees +acknowledgments +addendum +additionalresources +address +advertisement +advertisersindex +affect +affiliation +afterword +agenda +agradecimentos +agradecimientos +aimsandscope +analysis +annexa +announcement +announcements +annualacknowledgementofmanuscriptreviewers +anotefromtheeditor +appendices +appendix +appendix1 +appendixa +appendixb +appointmentsandstaffchanges +approximation +apresentacao +article +articlenumber +articles +articlesofsignificantinterestselectedfromthisissuebytheeditors +associationnews +ataglance +atribute +attention +authorguidelines +authorindex +authorindexforvolume81 +authorreply +authors +authorsreply +authorsresponse +avantpropos +award +awardsappointmentsannouncements +backcover +background +backmatter +berichtigung +besprechungen +bibliografia +bibliographie +bibliography +bigdata +blankpage +blood +boardoftrustees +booknotes +booknotices +bookofabstracts +bookreview +bookreviews +bookreviewsandnotices +bookreviewssection +booksreceived +buchbesprechung +buchbesprechungen +bulletin +calendar +calendarofevents +calendarofmeetings +callforarticles +callforpapers +casereport +casereports +casestudy +chairmansopeningremarks +changes +chaos +chapter1 +chapter10 +chapter1introduction +chapter2 +chapter7 +chapteri +chapterone +chapteroneintroduction +chaptertwo +chapterx +citation +classes +classified +classifieds +closingremarks +collaborateurs +comment +commentaries +commentary +commentaryon +commenton +comments +commentto +committee +communication +communications +communicationstotheeditor +communiquedepresse +community +components +comptesrendus +computerscience +concludingremarks +conclusion +conclusions +conferencereport +congratulations +congresscalendar +conservation +content +contents +context +continuingeducation +continuingmedicaleducation +contributors +copyright +copyrightform +copyrightnotice +correction +corrections +correspondence +corrigenda +corrigendum +councilminutes +cover +coverimage +currentresearch +curriculumvitae +danksagung +dearreaders +decisionmaking +dedication +dedicatoria +definition +description +discussion +diskussion +distribution +documents +ear +economics +editorial +editorialadvisoryboard +editorialannouncement +editorialboard +editorialcomment +editorialcomments +editorialconsultants +editoriale +editorialeditorial +editorialforeword +editorialinformation +editorialintroduction +editorialintroductions +editorialnote +editorialnotes +editorialpreface +editorials +editorialsoftwaresurveysection +editorialstaff +editorialstatement +editorinchief +editors +editorschoice +editorscomment +editorscomments +editorscorner +editorscorrespondence +editorsforeword +editorsintroduction +editorsletter +editorsnote +editorsnotes +editorspage +editorspicks 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+indexofauthorsandtitles +indice +indicegeneral +informationforauthors +informationtoauthors +inhalt +inhaltsverzeichnis +inleiding +inmemoriam +inreply +inresponse +insidethisissue +institutenews +instructionsforauthors +instructionstoauthors +interview +inthestudy +inthisissue +introducao +introduccion +introduction +introductionandoverview +introductiongenerale +introductiontotheissue +introductiontothespecialissue +introductorycomments +introductoryremarks +introduzione +inventions +invitedcommentary +issuesandevents +jobdescription +journalclub +journalscan +keywords +kurzkommentiert +languageteaching +lecture +letter +letterfromtheeditor +letterfromtheeditorinchief +letterfromtheeditors +letterfromthepresident +letters +letterstotheeditor +letterstotheeditors +lettertotheeditor +lettertotheeditors +liminaire +linearalgebra +linearregression +links +listedestableaux +listofabbreviations +listofcontributors +listoffigures +listofparticipants +listofpublications +listofreferees +listofreviewers +listoftables +literacy +literatur +literature +literaturecited +literaturereview +literaturrundschau +literaturverzeichnis +litteraturverzeichniss +livresrecus +lucina +lungcancer +magazin +maintenance +materials +materialsafetydatasheet +materialsandmethods +medicinalchemistry +meetingabstracts +meetingreport +meetings +meetingsandconferences +meetingsofinterest +membershipapplication +memoranda +memorandum +messagefromgeneralcochairs +messagefromthechairs +messagefromtheeditor +messagefromtheeditorinchief +messagefromthepresident +messagefromtheprogramchairs +messagefromtheprogramcochairs +metaanalysis +miscellanea +miscellaneous +miscellany +missionstatement +motivation +mrsnews +name +newbooks +newlyelectedmembersofthecollege +newproducts +news +newsandnotes +newsandreviews +newsandviews +newsbriefs +newsinbrief +newsnotes +newsviews +noii +note +notefromtheeditor +notes +notesandcomments +notesandnews +notesdelecture +notesforcontributors +notesoncontributors 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+referenciasbibliograficas +regression +rehabilitation +rejoinder +remerciements +reply +replybyauthors +researchresearchers +resenas +resources +response +responsetothelettertotheeditor +results +resume +resumen +resumes +resumo +retraction +review +reviewarticle +revieweracknowledgement +revieweracknowledgement2013 +reviewers +reviewessay +reviews +reviewsanddescriptionsoftablesandbooks +reviewsofbooks +rezension +rezensionen +safety +section +security +selectedbibliography +shortcommunication +shorternotices +shortnotices +socialengineering +sociology +sommaire +sommario +specialreport +specialsection +specifications +spistresci +subjectindex +subscriptions +suggestedreadings +sumario +summaries +summariesofkeyjournalarticles +summary +summaryofproceedings +summer +sun +supplementarymaterial +symposium +symptom +synthese +tabledesmatieres +tableofcontents +tableofcontentsandprologue +technicalreport +theauthors +theauthorsreply +thebasics +theeditorsdesk +thefirstauthorreplies +thelancet +theoreticalbackground +thetimes +theworldbank +theyearinreview +thismonthin +thismonthinthejournal +timemanagement +titeleiinhaltsverzeichnis +title +titlepage +titlepagei +tocorrespondents +totheeditor +unitedkingdom +unitednations +unitedstates +upcomingevents +vorwort +website +welcome +whatshappening +whatsnew +workscited +yourquestionsanswered +zudiesemheft +zusammenfassung |