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
|
#!/usr/bin/env python3
"""
This file started life as an ipython log file
Ugh, it needs to be copied to ../../python (with ./files/) to actually run. Derp.
"""
import os
import datetime
import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException
from fatcat_openapi_client import *
from fatcat_tools import *
import datetime
# setup env
#admin_id = "aaaaaaaaaaaabkvkaaaaaaaaae"
#local_conf = fatcat_openapi_client.Configuration()
#local_conf.host = 'http://localhost:9411/v0'
#local_api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(local_conf))
#api = local_api
api = authenticated_api(
'http://localhost:9411/v0',
# token is an optional kwarg (can be empty string, None, etc)
token=os.environ.get("FATCAT_API_AUTH_TOKEN"))
def upsert_release(doi, fname):
"""
Tries to fetch a release by doi from the API. If it can't be find, is
created from the referenced local JSON file (stripping a bunch of fields if
necessary).
Either way, returns ident
"""
try:
r = api.lookup_release(doi=doi)
print("release already existed: {}".format(doi))
return r.ident
except ApiException:
pass
r = entity_from_json(open(fname, 'r').read(), ReleaseEntity)
r.ident = None
r.release_rev = None
r.container_id = None
r.container = None
r.work_id = None
if r.release_type == 'journal-article':
r.release_type = 'article-journal'
r.edit_extra = dict(source="copied from old production as a demo")
files = [f for f in r.files]
print("bootstrapping release: {}".format(doi))
eg = api.create_editgroup(Editgroup())
resp = api.create_release(r, editgroup_id=eg.editgroup_id)
for f in files:
f.ident = None
f.revision = None
f.release_ids = [resp.ident]
files_resp = api.create_file_batch(files, editgroup_id=eg.editgroup_id)
api.accept_editgroup(eg.editgroup_id)
return resp.ident
def upsert_container(issnl, fname):
"""
Same as upsert_release, but for containers (by issnl)
"""
try:
c = api.lookup_container(issnl=issnl)
print("container already existed: {}".format(issnl))
return c.ident
except ApiException:
pass
c = entity_from_json(open(fname, 'r').read(), ContainerEntity)
c.ident = None
c.release_rev = None
c.container_id = None
c.edit_extra = dict(source="copied from old production as a demo")
print("bootstrapping container: {}".format(issnl))
eg = api.create_editgroup(Editgroup())
resp = api.create_container(c, editgroup_id=eg.editgroup_id)
api.accept_editgroup(eg.editgroup_id)
return resp.ident
def math_universe():
#c_ident = upsert_container("0015-9018", "files/foundations_of_physics.json")
ident = upsert_release("10.1007/s10701-007-9186-9", "files/math_universe.json")
base = api.get_release(ident, expand="files")
#base.container_id = c_ident
files = [api.get_file(f.ident) for f in base.files]
if len(files) <= 1:
print("already updated math_universe, skipping")
return
# create the pre-print version
preprint = api.get_release(base.ident)
preprint.doi = None
preprint.ident = None
preprint.revision = None
preprint.doi = None
preprint.container = None
preprint.publisher = None
preprint.volume = None
preprint.pages = None
preprint.wikidata_qid = None
preprint.arxiv_id = "0704.0646v2"
preprint.container_id = None
preprint.extra = dict(arxiv=dict(section='gr-qc'))
preprint.release_date = datetime.date(2007, 10, 8)
preprint.release_status = 'submitted'
preprint.work_id = base.work_id
eg = api.create_editgroup(Editgroup(description="math universe pre-print and file assignment"))
resp = api.create_release(preprint, editgroup_id=eg.editgroup_id)
files[1].release_ids = [resp.ident]
files[2].release_ids = [resp.ident]
files[3].release_ids = []
files[4].release_ids = []
api.update_file(files[1].ident, files[1], editgroup_id=eg.editgroup_id)
api.update_file(files[2].ident, files[2], editgroup_id=eg.editgroup_id)
api.update_file(files[3].ident, files[3], editgroup_id=eg.editgroup_id)
api.update_file(files[4].ident, files[4], editgroup_id=eg.editgroup_id)
api.update_release(base.ident, base, editgroup_id=eg.editgroup_id)
api.accept_editgroup(eg.editgroup_id)
# ok, that seems to have split it well enough
# Next, a distill.pub work
def distill_pub():
# pub,distill)/2017/momentum 20180613072149 https://distill.pub/2017/momentum/ text/html 200 4PP5AXYVD3VBB5BYYO4XK3FJXUR6Z46V 87161
# Why Momentum Really Works
# april 4, 2017
# Gabriel Goh
# orcid: 0000-0001-5021-2683
#c_ident = upsert_container("2476-0757", "files/distill_pub.json")
ident = upsert_release("10.23915/distill.00006", "files/distill_momentum.json")
momentum_works = api.get_release(ident, expand="files")
eg = api.create_editgroup(Editgroup(description="distill article enrichment"))
#goh = CreatorEntity(display_name="Gabriel Goh", orcid="0000-0001-5021-2683")
#goh = api.create_creator(goh, editgroup_id=eg.editgroup_id)
#distill = ContainerEntity(name="Distill", issnl="2476-0757", publisher="Distill", wikidata_qid="Q36437840")
#distill = api.create_container(distill, editgroup_id=eg.editgroup_id)
momentum_works.abstracts = [ReleaseEntityAbstracts(mimetype="text/plain", lang="en", content="We often think of Momentum as a means of dampening oscillations and speeding up the iterations, leading to faster convergence. But it has other interesting behavior. It allows a larger range of step-sizes to be used, and creates its own oscillations. What is going on?")]
#momentum_works.contribs = [ReleaseContrib(raw_name="Gabriel Goh", role='author', index=0, creator_id=goh.ident)]
momentum_works = api.update_release(momentum_works.ident, momentum_works, editgroup_id=eg.editgroup_id)
#momentum_works.container_id = c_ident
momentum_page = FileEntity(sha1='e3dfd05f151eea10f438c3b9756ca9bd23ecf3d5', mimetype='text/html')
momentum_page.urls = [FileEntityUrls(url="https://distill.pub/2017/momentum/", rel="publisher"), FileEntityUrls(url="http://web.archive.org/web/20180613072149/https://distill.pub/2017/momentum/", rel="webarchive")]
momentum_page.release_ids = [momentum_works.ident]
api.create_file(momentum_page, editgroup_id=eg.editgroup_id)
api.accept_editgroup(eg.editgroup_id)
def dlib_example():
# and now a d-lib exammple
#c_ident = upsert_container("1082-9873", "files/dlib.json")
ident = upsert_release("10.1045/november14-jahja", "files/dlib_example.json")
dlib = api.get_release(ident)
eg = api.create_editgroup(Editgroup(description="enriching d-lib article"))
#authors = [api.create_creator(CreatorEntity(display_name=a.raw_name), editgroup_id=eg.editgroup_id) for a in dlib.contribs]
#for i in range(3):
# dlib.contribs[i].creator_id = authors[i].ident
#dlib.container_id = c_ident
#r = api.update_release(dlib.ident, dlib, editgroup_id=eg.editgroup_id)
dlib_page = FileEntity(sha1='a637f1d27d9bcb237310ed29f19c07e1c8cf0aa5', mimetype='text/html')
dlib_page.urls = [FileEntityUrls(url="http://www.dlib.org/dlib/november14/jahja/11jahja.html", rel="publisher"), FileEntityUrls(url="http://web.archive.org/web/20180602033542/http://www.dlib.org/dlib/november14/jahja/11jahja.html", rel="webarchive")]
dlib_page.release_ids = [dlib.ident]
api.create_file(dlib_page, editgroup_id=eg.editgroup_id)
api.accept_editgroup(eg.editgroup_id)
# TODO: the actual web file here?
math_universe()
#distill_pub()
#dlib_example()
|
