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
|
import sys
import json
import sqlite3
import itertools
import fatcat_client
from fatcat_tools.importer_common import FatcatImporter
#row = row.split('\t')
#assert len(row) == 2
#sha1 = row[0].replace('sha1:')
#sha1 = base64.b16encode(base64.b32decode(sha1)).lower()
#print(sha1)
#dois = [d.lower() for d in json.loads(row[1])]
class FatcatMatchedImporter(FatcatImporter):
"""
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, host_url, skip_file_update=False, default_mime=None,
default_link_rel="web"):
super().__init__(host_url)
self.default_mime = default_mime
self.default_link_rel = default_link_rel
self.skip_file_update = skip_file_update
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 fatcat_client.FileEntityUrls(url=raw, rel=rel)
def parse_matched_dict(self, obj):
sha1 = obj['sha1']
dois = [d.lower() for d in obj.get('dois', [])]
# lookup sha1, or create new entity
fe = None
if not self.skip_file_update:
try:
fe = self.api.lookup_file(sha1=sha1)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
if fe is None:
fe = fatcat_client.FileEntity(
sha1=sha1,
releases=[],
urls=[],
)
# 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)
if len(re_list) == 0:
return None
if fe.releases == set(re_list):
return None
re_list.update(fe.releases)
fe.releases = list(re_list)
# parse URLs and CDX
existing_urls = [feu.url for feu in fe.urls]
for url in obj.get('url', []):
if url not in existing_urls:
url = self.make_url(url)
if url != None:
fe.urls.append(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
if wayback not in existing_urls:
fe.urls.append(
fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
if original not in existing_urls:
url = self.make_url(original)
if url != None:
fe.urls.append(url)
if obj.get('size') != None:
fe.size = int(obj['size'])
fe.sha256 = obj.get('sha256', fe.sha256)
fe.md5 = obj.get('md5', fe.sha256)
if obj.get('mimetype') is None:
if fe.mimetype is None:
fe.mimetype = self.default_mime
else:
fe.mimetype = obj.get('mimetype')
return fe
def create_row(self, row, editgroup=None):
obj = json.loads(row)
fe = self.parse_matched_dict(obj)
if fe is not None:
if fe.ident is None:
self.api.create_file(fe, editgroup=editgroup)
self.insert_count = self.insert_count + 1
else:
self.api.update_file(fe.ident, fe, editgroup=editgroup)
self.update_count = self.update_count + 1
def create_batch(self, batch, editgroup=None):
"""Reads and processes in batches (not API-call-per-line)"""
objects = [self.parse_matched_dict(json.loads(l))
for l in batch if l != None]
new_objects = [o for o in objects if o != None and o.ident == None]
update_objects = [o for o in objects if o != None and o.ident != None]
for obj in update_objects:
self.api.update_file(obj.ident, obj, editgroup=editgroup)
if len(new_objects) > 0:
self.api.create_file_batch(new_objects, autoaccept="true", editgroup=editgroup)
self.update_count = self.update_count + len(update_objects)
self.insert_count = self.insert_count + len(new_objects)
|
