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
|
import fatcat_openapi_client
from fatcat_tools.normal import clean_doi
from .common import SANE_MAX_RELEASES, SANE_MAX_URLS, EntityImporter, make_rel_url
class MatchedImporter(EntityImporter):
"""
Importer for "file to crossref DOI" matches.
These matches are currently generated by Internet Archive hadoop jobs
written in scala (part of the 'sandcrawler' repo/project), but could be
generated by other parties as well.
Input format is JSON with keys:
- dois (list)
- sha1 (hex)
- md5 (hex)
- sha256 (hex)
- size (int)
- cdx (list of objects)
- dt (optional; if included creates wayback link)
- url
- mimetype
- urls (list of strings... or objects?)
Future handlings/extensions:
- core_id, wikidata_id, pmcid, pmid: not as lists
"""
def __init__(self, api, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Import of large-scale file-to-release match results. Source of metadata varies."
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.MatchedImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mimetype = kwargs.get("default_mimetype", None)
def want(self, raw_record):
return True
def parse_record(self, obj):
dois = [d.lower() for d in obj.get('dois', [])]
# lookup dois
re_list = set()
for doi in dois:
doi = clean_doi(doi)
if not doi:
self.counts['skip-bad-doi'] += 1
return None
try:
re = self.api.lookup_release(doi=doi)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
#print("DOI not found: {}".format(doi))
pass
else:
re_list.add(re.ident)
# look up other external ids
for extid_type in ('arxiv', 'pmid', 'pmcid', 'jstor', 'wikidata_qid', 'core', 'isbn13', 'ark'):
extid = obj.get(extid_type)
if extid:
try:
re = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
pass
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
self.counts['skip-no-releases'] += 1
return None
if len(release_ids) > SANE_MAX_RELEASES:
self.counts['skip-too-many-releases'] += 1
return None
# parse URLs and CDX
urls = set()
for url in obj.get('urls', []):
url = make_rel_url(url, default_link_rel=self.default_link_rel)
if url is not None:
urls.add(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
if cdx.get('dt'):
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
urls.add(("webarchive", wayback))
url = make_rel_url(original, default_link_rel=self.default_link_rel)
if url is not None:
urls.add(url)
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
if len(urls) == 0:
self.counts['skip-no-urls'] += 1
return None
if len(urls) > SANE_MAX_URLS:
self.counts['skip-too-many-urls'] += 1
return None
size = obj.get('size')
if size:
size = int(size)
mimetype = obj.get('mimetype', self.default_mimetype)
if not mimetype and urls:
if urls[0].url.endswith('.pdf'):
mimetype = 'application/pdf'
fe = fatcat_openapi_client.FileEntity(
md5=obj.get('md5'),
sha1=obj['sha1'],
sha256=obj.get('sha256'),
size=size,
mimetype=mimetype,
release_ids=release_ids,
urls=urls,
)
return fe
def try_update(self, fe):
# lookup sha1, or create new entity
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if not existing:
return True
combined_release_ids = list(set(fe.release_ids + existing.release_ids))
if set(combined_release_ids) == set(existing.release_ids) and len(existing.urls) > 0:
# no new release matches *and* there are already existing URLs
self.counts['exists'] += 1
return False
# check for edit conflicts
if existing.ident in [e.ident for e in self._edits_inflight]:
self.counts['skip-update-inflight'] += 1
return False
# minimum viable "existing" URL cleanup to fix dupes and broken links:
# remove 'None' wayback URLs, and set archive.org rel 'archive'
existing.urls = [u for u in existing.urls if not ('://web.archive.org/web/None/' in u.url)]
for i in range(len(existing.urls)):
u = existing.urls[i]
if u.rel == 'repository' and '://archive.org/download/' in u.url:
existing.urls[i].rel = 'archive'
# special case: if importing *new* from archive.org arxiv collections,
# blow away any existing release_id mappings; this is a direct arxiv_id
# map. This *should* be safe to run in all matched imports.
is_arxiv = False
for u in fe.urls:
if 'archive.org/download/arxiv' in u.url.lower():
is_arxiv = True
break
if is_arxiv and fe.release_ids:
existing.release_ids = fe.release_ids
# merge the existing into this one and update
existing.urls = list(set([(u.rel, u.url) for u in fe.urls + existing.urls]))
existing.urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
if len(existing.urls) > SANE_MAX_URLS:
self.counts['skip-update-too-many-url'] += 1
return None
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
if len(existing.release_ids) > SANE_MAX_RELEASES:
self.counts['skip-update-too-many-releases'] += 1
return None
existing.mimetype = existing.mimetype or fe.mimetype
existing.size = existing.size or fe.size
existing.md5 = existing.md5 or fe.md5
existing.sha1 = existing.sha1 or fe.sha1
existing.sha256 = existing.sha256 or fe.sha256
edit = self.api.update_file(self.get_editgroup_id(), existing.ident, existing)
self._edits_inflight.append(edit)
self.counts['update'] += 1
return False
def insert_batch(self, batch):
self.api.create_file_auto_batch(fatcat_openapi_client.FileAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
|
