1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
|
"""
Contrib related comparisons.
Example: NgramContribMatcher, which compares two normalized raw name tokens
with a jaccard index.
matcher = ContribMatcher(cmp=JaccardIndexThreshold(0.5),
pipeline=Pipeline([
lambda rc: rc.raw_name,
str.strip,
str.lower,
Ngram(n=3),
set,
]))
result = matcher.compare(a, b)
...
Some notes from the dataset.
* 692,893,828 contribs
* 64,680,311 uniq
Top contrib names, many have their name on datasets, which explains the high
number.
3069752 Kessy Abarenkov
2383819 Leho Tedersoo
2383748 Karl-Henrik Larsson
2383745 Urmas Kõljalg
2383699 Mohammad Bahram
2383692 Martin Ryberg
2382832 R. Henrik Nilsson
1702455 Markus Döring
1702427 Tom May
1702415 Dmitry Schigel
1702391 Santiago Sánchez-Ramírez
841475 GLIS Of The ITPGRFA
682144 James Scott
682053 Michael Weiss
681404 Susumu Takamatsu
681388 A. Elizabeth Arnold
681347 Artur Alves
681341 Ellen Larsson
681338 Maarja Öpik
681335 Ursula Eberhardt
681324 Nhu Nguyen
681293 Otto Miettinen
681292 Viacheslav Spirin
681287 Gareth W. Griffith
681283 Bálint Dima
681278 Ursula Peintner
681276 Tuula Niskanen
681276 Olinto Liparini Pereira
681275 Kare Liimatainen
"""
import collections
import functools
import itertools
import logging
import operator
import re
import string
from typing import Any, Callable, List, Optional, Set
import jellyfish
import thefuzz
from fatcat_openapi_client import ReleaseContrib
logger = logging.getLogger("fuzzycat")
class Ngram:
"""
Turn a string into a list of overlapping tokens.
"""
def __init__(self, n: int = 3):
if n < 1:
raise ValueError("positive n required")
self.n = n
def __call__(self, s: str) -> List[str]:
if 0 < len(s) < self.n:
return [s]
return [s[i:i + self.n] for i in range(len(s) - self.n + 1)]
class JaccardIndexThreshold:
"""
A Jaccard index threshold that can be used to compare two sets. Two empty
sets are equal.
"""
def __init__(self, threshold: float = 0.5, verbose=False):
self.threshold = threshold
self.verbose = verbose
def __call__(self, a: Set, b: Set) -> bool:
if len(a) == 0 and len(b) == 0:
return True
index = len(a & b) / len(a | b)
if self.verbose:
logger.debug("[jaccard] {}".format(index))
return index >= self.threshold
class FuzzyStringSimilarity:
"""
For two sets of strings, run fuzzy matching with "thefuzz" -
https://github.com/seatgeek/thefuzz, which among other things uses
Levenshtein distance.
The min ratio can range from 0 to 100 (with 100 allowing exact matches
only).
"""
def __init__(self, min_ratio=75):
self.min_ratio = min_ratio
def __call__(self, a: Set, b: Set) -> bool:
agg = 0
for v in a:
match, score = thefuzz.exctractOne(v, b)
agg += score
return score > self.min_ratio
class Pipeline:
"""
A list of functions to execute, f -> g -> h, etc. Note that the output
type of f needs to match the input type of g, etc.
"""
def __init__(self, pipeline: Optional[List[Any]] = None, verbose: bool = False):
self.verbose = verbose
if pipeline is None:
self.pipeline = [
lambda v: v,
]
else:
self.pipeline = pipeline
def run(self, value: Any) -> Any:
v = value
for i, f in enumerate(self.pipeline, start=1):
v = f(v)
if self.verbose:
logger.debug("[{}/{}] {}".format(i, len(self.pipeline), v))
return v
def __call__(self, value: Any, verbose: bool = False) -> Any:
self.verbose = verbose
return self.run(value)
# default_release_contrib_pipeline normalizes the raw name.
default_release_contrib_pipeline = Pipeline([
lambda rc: rc.raw_name,
str.strip,
str.lower,
])
# default_release_contrib_list_pipeline turns contribs list into a contrib set.
default_release_contrib_list_pipeline = Pipeline([
lambda seq: set((c.raw_name for c in seq)),
])
class ContribMatcher:
"""
Compare two contrib entities and determine a match status, based on some
configuration. The final values of the `pipeline` will be compared with
`cmp`, which by default is equality.
Other `cmp` options may generate ngrams and use jaccard index with some
threshold or decide on a string similarity metric.
This is essentially just a shell, the various comparison methods live in
the tuple (pipeline, cmp).
"""
def __init__(self,
pipeline: Optional[List[Any]] = default_release_contrib_list_pipeline,
cmp: Callable[[Any, Any], bool] = operator.__eq__):
self.pipeline = pipeline
self.cmp = cmp
def compare(self, a: ReleaseContrib, b: ReleaseContrib) -> bool:
"""
Compare returns True, if a and b are considered the same, given a
transformation pipeline and a comparison operation.
"""
u = self.pipeline(a)
v = self.pipeline(b)
return self.cmp(u, v)
class ContribListMatcher:
"""
Compare two lists of contribs. Each contrib entry is passed through the
same pipeline.
Often two issues (separate or combined).
- contrib missing, e.g.
- "Gentle Sunder Shrestha", "Gentle S Shrestha", "S. Shrestha", "Gentle Shrestha", ...
"""
def __init__(self,
pipeline: Optional[List[Any]] = default_release_contrib_list_pipeline,
cmp: Callable[[Any, Any], bool] = JaccardIndexThreshold(1.0)):
self.pipeline = pipeline
self.cmp = cmp
def compare(self,
a: List[ReleaseContrib],
b: List[ReleaseContrib],
verbose: bool = False) -> bool:
"""
Compare two lists of contribs, pass each one through the pipeline. The
result may be a list or any other type. The comparison function needs
to be compatible.
"""
u = self.pipeline(a, verbose=verbose)
v = self.pipeline(b, verbose=verbose)
return self.cmp(u, v)
def cleanup_single_ws(s: str) -> str:
return re.sub(r"[ ]{2,}", " ", s)
def cleanup_remove_ws(s: str) -> str:
return re.sub(r"[\n\r\t\s]*", '', s)
def cleanup_keep_letters_digits_ws(s: str) -> str:
return ''.join((c for c in s if c in string.ascii_letters + string.digits + " "))
def test_cleanup_single_ws():
Case = collections.namedtuple("Case", "s result")
cases = (
Case("", ""),
Case("abc", "abc"),
Case("abc abc", "abc abc"),
Case("abc abc", "abc abc"),
Case(" abc abc", " abc abc"),
Case(" abc abc", " abc abc"),
)
for c in cases:
assert c.result == cleanup_single_ws(c.s)
def test_cleanup_remove_ws():
Case = collections.namedtuple("Case", "s result")
cases = (
Case("", ""),
Case("abc", "abc"),
Case("abc abc", "abcabc"),
Case("abc abc", "abcabc"),
Case(" abc abc", "abcabc"),
)
for c in cases:
assert c.result == cleanup_remove_ws(c.s), c
def test_ngram():
Case = collections.namedtuple("Case", "s n result")
cases = (
Case("", 1, []),
Case("", 2, []),
Case("a", 2, ["a"]),
Case("ab", 2, ["ab"]),
Case("abcdef", 2, ['ab', 'bc', 'cd', 'de', 'ef']),
Case("abcdef", 4, ['abcd', 'bcde', 'cdef']),
Case("Nina Rogo", 3, ["Nin", "ina", "na ", "a R", " Ro", "Rog", "ogo"]),
)
for c in cases:
ngram = Ngram(n=c.n)
assert ngram(c.s) == c.result
def test_pipeline():
Case = collections.namedtuple("Case", "pipeline input result")
cases = (Case(Pipeline([lambda v: v["a"], str.strip, str.lower,
Ngram(n=3), set]), {"a": " X123 "}, {'123', 'x12'})),
for c in cases:
result = c.pipeline(c.input)
assert result == c.result
def test_jaccard_index_threshold():
Case = collections.namedtuple("Case", "a b threshold result")
cases = (
Case(set(), set(), 1.0, True),
Case(set(), set(["a"]), 1.0, False),
Case(set(["a"]), set(["a"]), 1.0, True),
Case(set(["a"]), set(["a", "b"]), 1.0, False),
Case(set(["a"]), set(["a", "b"]), 0.5, True),
Case(set(["a"]), set(["a", "b", "c"]), 0.5, False),
)
for c in cases:
jit = JaccardIndexThreshold(threshold=c.threshold)
result = jit(c.a, c.b)
assert result == c.result
def test_ngram_contrib_matcher(caplog):
Case = collections.namedtuple("Case", "a b result")
cases = (
Case(
ReleaseContrib(raw_name="Jane Austen"),
ReleaseContrib(raw_name="J.Austen"),
True,
),
Case(
ReleaseContrib(raw_name="Fjodor Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor M. Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor Michailowitsch Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
)
matcher = ContribMatcher(cmp=JaccardIndexThreshold(0.4, verbose=True),
pipeline=Pipeline([
lambda rc: rc.raw_name,
str.strip,
str.lower,
cleanup_remove_ws,
cleanup_keep_letters_digits_ws,
Ngram(n=3),
set,
],
verbose=True))
for c in cases:
with caplog.at_level(logging.DEBUG):
result = matcher.compare(c.a, c.b)
assert result == c.result
def test_jellyfish_soundex_contrib_matcher(caplog):
Case = collections.namedtuple("Case", "a b result")
cases = (
Case(
ReleaseContrib(raw_name="Jane Austen"),
ReleaseContrib(raw_name="J.Austen"),
True,
),
Case(
ReleaseContrib(raw_name="Fjodor Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor M. Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor Michailowitsch Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
)
matcher = ContribMatcher(cmp=JaccardIndexThreshold(0.3, verbose=True),
pipeline=Pipeline([
lambda rc: rc.raw_name,
str.strip,
str.lower,
functools.partial(re.sub, r"[.;]", " "),
cleanup_keep_letters_digits_ws,
lambda s: set((jellyfish.soundex(v) for v in s.split())),
],
verbose=True))
for c in cases:
with caplog.at_level(logging.DEBUG):
result = matcher.compare(c.a, c.b)
assert result == c.result
def test_jellyfish_nysiis_contrib_matcher(caplog):
Case = collections.namedtuple("Case", "a b result")
cases = (
Case(
ReleaseContrib(raw_name="Jane Austen"),
ReleaseContrib(raw_name="J.Austen"),
True,
),
Case(
ReleaseContrib(raw_name="Fjodor Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor M. Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
Case(
ReleaseContrib(raw_name="Fjodor Michailowitsch Dostojewski"),
ReleaseContrib(raw_name="Fyodor Dostoevsky"),
False,
),
)
matcher = ContribMatcher(cmp=JaccardIndexThreshold(0.3, verbose=True),
pipeline=Pipeline([
lambda rc: rc.raw_name,
str.strip,
str.lower,
functools.partial(re.sub, r"[.;]", " "),
cleanup_keep_letters_digits_ws,
lambda s: set((jellyfish.nysiis(v) for v in s.split())),
],
verbose=True))
for c in cases:
with caplog.at_level(logging.DEBUG):
result = matcher.compare(c.a, c.b)
assert result == c.result
def test_default_contrib_list_matcher(caplog):
Case = collections.namedtuple("Case", "a b result")
cases = (
Case(
[],
[],
True,
),
Case(
[ReleaseContrib(raw_name="Michael Jordan")],
[ReleaseContrib(raw_name="Michael Jordan")],
True,
),
Case(
[ReleaseContrib(raw_name="Michael Jordan")],
[ReleaseContrib(raw_name="michael jordan")],
False,
),
Case(
[ReleaseContrib(raw_name="Amadeu Llebaria")],
[ReleaseContrib(raw_name="A. Llebaria")],
False,
),
)
matcher = ContribListMatcher()
for c in cases:
with caplog.at_level(logging.DEBUG):
result = matcher.compare(c.a, c.b, verbose=True)
assert result == c.result
|