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
|
import sys
import json
import base64
import itertools
import fatcat_openapi_client
from .common import EntityImporter, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS, b32_hex
class IngestFileResultImporter(EntityImporter):
def __init__(self, api, require_grobid=True, **kwargs):
eg_desc = kwargs.get('editgroup_description',
"Files crawled from web using sandcrawler ingest tool")
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileResultImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
assert self.default_link_rel
self.default_mimetype = kwargs.get("default_mimetype", None)
self.do_updates = kwargs.get("do_updates", False)
self.require_grobid = require_grobid
if self.require_grobid:
print("Requiring GROBID status == 200")
else:
print("NOT checking GROBID success")
def want(self, row):
if self.require_grobid and not row.get('grobid', {}).get('status_code') == 200:
return False
if row.get('hit') == True and row.get('file_meta'):
return True
else:
return False
def parse_record(self, row):
request = row['request']
fatcat = request.get('fatcat')
file_meta = row['file_meta']
# identify release by fatcat ident or extid lookup
release_ident = None
if fatcat and fatcat.get('release_ident'):
release_ident = fatcat.get('release_ident')
elif request.get('ext_ids'):
# if no fatcat ident, try extids
for extid_type in ('doi', 'pmid', 'pmcid', 'arxiv'):
extid = request['ext_ids'].get(extid_type)
if not extid:
continue
try:
release = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status == 404:
continue
elif err.status == 400:
self.counts['warn-extid-invalid'] += 1
continue
release_ident = release.ident
break
if not release:
self.counts['skip-release-not-found'] += 1
cdx = row.get('cdx')
if not cdx:
return None
url = make_rel_url(cdx['url'], self.default_link_rel)
if not url:
self.counts['skip-url'] += 1
return None
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['datetime'],
cdx['url'])
urls = [url, ("webarchive", wayback)]
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
fe = fatcat_openapi_client.FileEntity(
md5=file_meta['md5hex'],
sha1=file_meta['sha1hex'],
sha256=file_meta['sha256hex'],
size=file_meta['size_bytes'],
mimetype=file_meta['mimetype'] or self.default_mimetype,
release_ids=[release_ident],
urls=urls,
)
if fatcat and fatcat.get('edit_extra'):
fe.edit_extra = fatcat['edit_extra']
if request.get('project'):
if not fe.edit_extra:
fe.edit_extra = dict()
fe.edit_extra['project'] = request['project']
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
if (fe.release_ids[0] in existing.release_ids) and existing.urls:
# TODO: could still, in theory update with the new URL?
self.counts['exists'] += 1
return False
if not self.do_updates:
self.counts['skip-update-disabled'] += 1
return False
# TODO: for now, never update
self.counts['skip-update-disabled'] += 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))
|
