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
|
import sys
import json
import sqlite3
import itertools
import fatcat_client
from .common import EntityImporter
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
- 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.get('editgroup_description',
"Import of large-scale file-to-release match results. Source of metadata varies.")
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.MatchedImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mime = kwargs.get("default_mime", None)
self.skip_file_updates = kwargs.get("skip_file_updates", False)
def make_url(self, raw):
rel = self.default_link_rel
# TODO: this is where we could map specific domains to rel types,
# and also filter out bad domains, invalid URLs, etc
if "//archive.org/" in raw or "//arxiv.org/" in raw:
# TODO: special-case the arxiv.org bulk mirror?
rel = "repository"
elif "//web.archive.org/" in raw or "//archive.is/" in raw:
rel = "webarchive"
return (rel, raw)
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:
try:
re = self.api.lookup_release(doi=doi)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
print("DOI not found: {}".format(doi))
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
return None
# parse URLs and CDX
urls = set()
for url in obj.get('url', []):
url = self.make_url(url)
if url != None:
urls.add(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
urls.add(("webarchive", wayback))
url = self.make_url(original)
if url != None:
urls.add(url)
urls = [fatcat_client.FileEntityUrls(rel, url) for (rel, url) in urls]
if len(urls) == 0:
return None
size = obj.get('size')
if size:
size = int(size)
fe = fatcat_client.FileEntity(
md5=obj.get('md5'),
sha1=obj['sha1'],
sha256=obj.get('sha256'),
size=size,
mimetype=obj.get('mimetype'),
release_ids=release_ids,
urls=urls,
)
return fe
def try_update(self, fe):
# lookup sha1, or create new entity
existing = None
if not self.skip_file_updates:
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
if not existing:
# new match; go ahead and insert
return True
fe.release_ids = list(set(fe.release_ids + existing.release_ids))
if set(fe.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
# merge the existing into this one and update
existing.urls = list(set(fe.urls + existing.urls))
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
existing.mimetype = existing.mimetype or fe.mimetype
existing.size = existing.size or fe.size
existing.md5 = existing.md5 or fe.md5
existing.sha256 = existing.sha256 or fe.sha256
self.api.update_file(existing.ident, existing)
self.counts['update'] += 1
return False
def insert_batch(self, batch):
self.api.create_file_batch(batch,
autoaccept=True,
description=self.editgroup_description,
extra=json.dumps(self.editgroup_extra))
|
