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
|
"""
This file contains simple high-level functions that call in to match, verify,
and unstructured parsing routines.
close_fuzzy_release_matches(release) -> List[FuzzyReleaseMatchResult]
close_fuzzy_biblio_matches(biblio) -> List[FuzzyReleaseMatchResult]
close_fuzzy_unstructured_matches(unstructured) -> List[FuzzyReleaseMatchResult]
Each function takes additional arguments:
es_client
fatcat_api_client
match_limit
Each also has a "closest" variant, which returns just the single highest-rated
match.
"""
from dataclasses import dataclass
from typing import Any, List, Optional
from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds
from fuzzycat.common import Reason, Status
from fuzzycat.entities import entity_to_dict
from fuzzycat.grobid_unstructured import grobid_parse_unstructured
from fuzzycat.matching import match_release_fuzzy
from fuzzycat.verify import verify
@dataclass
class FuzzyReleaseMatchResult:
status: Status
reason: Reason
release: ReleaseEntity
# this map used to establish priority order of verified matches
STATUS_SORT = {
Status.TODO: 0,
Status.EXACT: 10,
Status.STRONG: 20,
Status.WEAK: 30,
Status.AMBIGUOUS: 40,
Status.DIFFERENT: 60,
}
def close_fuzzy_release_matches(release: ReleaseEntity,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> Optional[FuzzyReleaseMatchResult]:
"""
This high-level helper function runs a fuzzy match (using elasticsearch),
verifies all the results, and returns the "closest" matching results (if
any).
es_client is required, and used in the matcing process.
fatcat_api_client is optional and used both for entity-to-dict conversion
efficiency and for fetching current entities from the fatcat API
match_limit sets the maximum result size from the inital fuzzy match call
Returns an empty list if there was no match of any kind, or a sorted list
of simple result objects (FuzzyReleaseMatchResult dataclass) with fields:
status: fuzzycat.common.Status
reason: fuzzycat.common.Reason
release: ReleaseEntity
Status is one of the fuzzycat.common.Status, with "strongest match" in this
sorted order:
- EXACT
- STRONG
- WEAK
- AMBIGUOUS
DIFFERENT and TODO matches are never returned.
Eg, if there is any EXACT match that is always returned; an AMBIGIOUS
result is only returned if all the candidate matches were ambiguous.
"""
candidates = match_release_fuzzy(release, size=match_limit, es=es_client)
if not candidates:
return None
release_dict = entity_to_dict(release, api_client=fatcat_api_client)
# list of tuple of (Verify, ReleaseEntity)
verified = [(
verify(release_dict, entity_to_dict(c, api_client=fatcat_api_client)),
c,
) for c in candidates]
# list of FuzzyReleaseMatchResult, with TODO and DIFFERENT removed
verified = [
FuzzyReleaseMatchResult(v[0].status, v[0].reason, v[1]) for v in verified
if v[0].status not in [Status.TODO, Status.DIFFERENT]
]
return sorted(verified, key=lambda v: STATUS_SORT[v.status])
def closest_fuzzy_release_match(release: ReleaseEntity,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> Optional[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_release_matches()
"""
matches = close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
def close_fuzzy_unstructured_matches(raw_citation: str,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Variation of close_fuzzy_release_matches() which first parses an
unstructured citation string, then finds close matches.
TODO: pass-through GROBID API configuration?
"""
release = grobid_parse_unstructured(raw_citation)
if not release:
return None
return close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
def closest_fuzzy_unstructured_match(raw_citation: str,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_release_matches()
"""
matches = close_fuzzy_unstructured_matches(
raw_citation,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
def biblio_to_release(biblio: dict) -> ReleaseEntity:
"""
Helper for close_fuzzy_biblio_matches() et al
"""
contribs = []
if biblio.get('authors'):
for a in biblio['authors']:
contribs.append(
ReleaseContrib(
raw_name=a.get('name'),
given_name=a.get('given_name'),
surname=a.get('surname'),
))
elif biblio.get('author_names'):
for a in biblio['author_names']:
contribs.append(ReleaseContrib(raw_name=a))
elif biblio.get('first_author'):
contribs.append(ReleaseContrib(raw_name=biblio['first_author']))
release = ReleaseEntity(
title=biblio.get("title"),
ext_ids=ReleaseExtIds(
doi=biblio.get("doi"),
pmid=biblio.get("pmid"),
pmcid=biblio.get("pmcid"),
arxiv=biblio.get("arxiv_id"),
),
volume=biblio.get("volume"),
issue=biblio.get("issue"),
pages=biblio.get("pages") or biblio.get("first_page"),
publisher=biblio.get("publisher"),
release_stage=biblio.get("release_stage"),
release_type=biblio.get("release_type"),
extra=dict(),
)
if biblio.get('journal'):
release.extra['container_name'] = biblio['journal']
elif biblio.get('conference'):
release.extra['container_name'] = biblio['conference']
if biblio.get('year'):
year = biblio['year']
if isinstance(year, str) and len(year) >= 4 and year[0:4].isdigit():
release.release_year = int(year[0:4])
elif isinstance(year, int):
release.release_year = year
elif biblio.get('date'):
date = biblio['date']
if isinstance(date, str) and len(date) >= 4 and date[0:4].isdigit():
release.release_year = int(date[0:4])
return release
def close_fuzzy_biblio_matches(biblio: dict,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Variation of close_fuzzy_release_matches() which takes bibliographic fields
as arguments.
Biblio fields which are handled include:
title
journal
or: conference
authors
name
given_name
surname
or: author_names (List[str])
or: first_author (str)
year
date
volume
issue
pages
or: first_page
publisher
doi
pmid
arxiv_id
release_type (eg, 'journal-article', 'book', 'dataset')
release_stage
"""
release = biblio_to_release(biblio)
return close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
def closest_fuzzy_biblio_match(biblio: dict,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_biblio_matches()
"""
matches = close_fuzzy_biblio_matches(
biblio,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
|
