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
|
#!/usr/bin/env python3
import sys
import json
import base64
import datetime
import fatcat_client
from fatcat.importer_common import FatcatImporter
MAX_ABSTRACT_BYTES=4096
class FatcatGrobidMetadataImporter(FatcatImporter):
def __init__(self, host_url, default_link_rel="web"):
super().__init__(host_url)
self.default_link_rel = default_link_rel
def parse_grobid_json(self, obj):
if not obj.get('title'):
return None
release = dict()
extra = dict()
if obj.get('abstract') and len(obj.get('abstract')) < MAX_ABSTRACT_BYTES:
abobj = dict(
mimetype="text/plain",
language=None,
content=obj.get('abstract').strip())
abstracts = [abobj]
else:
abstracts = None
contribs = []
for i, a in enumerate(obj.get('authors', [])):
c = dict(raw_name=a['name'], role="author")
contribs.append(fatcat_client.ReleaseContrib(
index=i,
raw_name=a['name'],
role="author",
extra=None))
refs = []
for raw in obj.get('citations', []):
cite_extra = dict()
ref = dict()
ref['key'] = raw.get('id')
if raw.get('title'):
ref['title'] = raw['title'].strip()
if raw.get('date'):
try:
year = int(raw['date'].strip()[:4])
ref['year'] = year
except:
pass
for key in ('volume', 'url', 'issue', 'publisher'):
if raw.get(key):
cite_extra[key] = raw[key].strip()
if raw.get('authors'):
cite_extra['authors'] = [a['name'] for a in raw['authors']]
if cite_extra:
cite_extra = dict(grobid=cite_extra)
else:
cite_extra = None
ref['extra'] = cite_extra
refs.append(ref)
release_type = "journal-article"
release_date = None
if obj.get('date'):
# TODO: only returns year, ever? how to handle?
release_date = datetime.datetime(year=int(obj['date'][:4]), month=1, day=1)
if obj.get('doi'):
extra['doi'] = obj['doi']
if obj['journal'] and obj['journal'].get('name'):
extra['container_name'] = obj['journal']['name']
extra['is_longtail_oa'] = True
# TODO: ISSN/eISSN handling? or just journal name lookup?
if extra:
extra = dict(grobid=extra)
else:
extra = None
re = fatcat_client.ReleaseEntity(
title=obj['title'].strip(),
contribs=contribs,
refs=refs,
publisher=obj['journal'].get('publisher'),
volume=obj['journal'].get('volume'),
issue=obj['journal'].get('issue'),
abstracts=abstracts,
extra=extra)
return re
# TODO: make this a common function somewhere
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_file_metadata(self, sha1_key, cdx, mimetype, file_size):
sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()
# lookup existing SHA1, or create new entity
try:
existing_file = self.api.lookup_file(sha1=sha1)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
existing_file = None
if existing_file:
# if file is already in here, presumably not actually long-tail
return None
fe = fatcat_client.FileEntity(
sha1=sha1,
size=int(file_size),
mimetype=mimetype,
releases=[],
urls=[],
)
# parse URLs and CDX
original = cdx['url']
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
fe.urls.append(
fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
original_url = self.make_url(original)
if original_url != None:
fe.urls.append(original_url)
return fe
def create_row(self, row, editgroup=None):
if not row:
return
fields = row.split('\t')
sha1_key = fields[0]
cdx = json.loads(fields[1])
mimetype = fields[2]
file_size = int(fields[3])
grobid_meta = json.loads(fields[4])
fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
re = self.parse_grobid_json(grobid_meta)
if fe and re:
release_entity = self.api.create_release(re, editgroup=editgroup)
# release ident can't already be in release list because we just
# created it
fe.releases.append(release_entity.ident)
file_entity = self.api.create_file(fe, editgroup=editgroup)
self.insert_count = self.insert_count + 1
# NB: batch mode not implemented
|
