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
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
|
New unpaywall snapshot from `2022-03-09`.
This will probably be the last unpaywall crawl? Will switch to openalex in the
future, because we can automate that ingest process, and run it on our own
schedule.
export SNAPSHOT=2022-03-09
export CRAWLVM=wbgrp-svc279.us.archive.org
export CRAWLNAME=UNPAYWALL-CRAWL-2022-04
## Download and Archive
wget 'https://unpaywall-data-snapshots.s3.us-west-2.amazonaws.com/unpaywall_snapshot_2022-03-09T083001.jsonl.gz'
# 2022-04-09 22:31:43 (98.9 KB/s) - ‘unpaywall_snapshot_2022-03-09T083001.jsonl.gz’ saved [29470830470/29470830470]
export SNAPSHOT=2022-03-09
ia upload unpaywall_snapshot_$SNAPSHOT unpaywall_snapshot_$SNAPSHOT*.jsonl.gz -m title:"Unpaywall Metadata Snapshot ($SNAPSHOT)" -m collection:ia_biblio_metadata -m creator:creator -m date:$SNAPSHOT
# if needed
scp unpaywall_snapshot_$SNAPSHOT*.jsonl.gz wbgrp-svc506.us.archive.org:/srv/sandcrawler/tasks
## Transform and Load
# in sandcrawler pipenv on sandcrawler1-vm (svc506)
cd /srv/sandcrawler/src/python
sudo su sandcrawler
pipenv shell
zcat /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT*.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT.ingest_request.json
# 34.9M 3:02:32 [3.19k/s]
cat /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
# 34.9M 5:23:15 [1.80k/s]
# Worker: Counter({'total': 34908779, 'insert-requests': 6129630, 'update-requests': 0})
# JSON lines pushed: Counter({'total': 34908779, 'pushed': 34908779})
So about 6.1M new ingest request rows.
## Dump new URLs, Transform, Bulk Ingest
COPY (
SELECT row_to_json(ingest_request.*)
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_file_result.ingest_type = ingest_request.ingest_type
AND ingest_file_result.base_url = ingest_request.base_url
WHERE
ingest_request.ingest_type = 'pdf'
AND ingest_request.link_source = 'unpaywall'
-- take "all time" instead of just this recent capture
-- AND date(ingest_request.created) > '2021-01-01'
AND (ingest_file_result.status IS NULL
OR ingest_file_result.status = 'no-capture')
) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2022-03-09.rows.json';
=> COPY 6025671
# transform
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.ingest_request.json
# 6.03M 0:03:26 [29.1k/s]
# enqueue for bulk processing
cat /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
## Check Pre-Crawl Status
Only the recent bulk ingest:
SELECT ingest_file_result.status, COUNT(*)
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_file_result.ingest_type = ingest_request.ingest_type
AND ingest_file_result.base_url = ingest_request.base_url
WHERE
ingest_request.ingest_type = 'pdf'
AND ingest_request.link_source = 'unpaywall'
AND date(ingest_request.created) > '2022-04-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
no-capture | 3330232
success | 2455102
redirect-loop | 197117
terminal-bad-status | 82618
no-pdf-link | 33046
blocked-cookie | 16078
link-loop | 6745
wrong-mimetype | 3416
wayback-error | 1385
empty-blob | 1142
cdx-error | 820
body-too-large | 292
bad-gzip-encoding | 281
wayback-content-error | 267
| 253
petabox-error | 215
skip-url-blocklist | 185
null-body | 179
spn2-cdx-lookup-failure | 89
gateway-timeout | 73
(20 rows)
After prior "TARGETED" crawl and bulk ingest finished:
status | count
-------------------------+---------
no-capture | 3330055
success | 2455279
redirect-loop | 197117
terminal-bad-status | 82618
no-pdf-link | 33046
blocked-cookie | 16079
link-loop | 6745
wrong-mimetype | 3416
wayback-error | 1385
empty-blob | 1142
cdx-error | 820
body-too-large | 292
bad-gzip-encoding | 281
wayback-content-error | 267
| 253
petabox-error | 215
skip-url-blocklist | 185
null-body | 179
spn2-cdx-lookup-failure | 89
gateway-timeout | 73
(20 rows)
Almost no change, which makes sense because of the `ingest_request.created`
filter.
## Dump Seedlist
Dump rows for crawling:
COPY (
SELECT row_to_json(t1.*)
FROM (
SELECT ingest_request.*, ingest_file_result as result
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_file_result.ingest_type = ingest_request.ingest_type
AND ingest_file_result.base_url = ingest_request.base_url
WHERE
ingest_request.ingest_type = 'pdf'
-- AND date(ingest_request.created) > '2022-04-01'
AND ingest_request.link_source = 'unpaywall'
AND (ingest_file_result.status = 'no-capture'
OR ingest_file_result.status = 'cdx-error'
OR ingest_file_result.status = 'wayback-error'
OR ingest_file_result.status = 'gateway-timeout'
OR ingest_file_result.status LIKE 'spn2-%'
)
AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%'
AND ingest_request.base_url NOT LIKE '%pubs.acs.org%'
AND ingest_request.base_url NOT LIKE '%ahajournals.org%'
AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%'
AND ingest_request.base_url NOT LIKE '%aip.scitation.org%'
AND ingest_request.base_url NOT LIKE '%academic.oup.com%'
AND ingest_request.base_url NOT LIKE '%tandfonline.com%'
AND ingest_request.base_url NOT LIKE '%.archive.org%'
AND ingest_request.base_url NOT LIKE '%://archive.org%'
AND ingest_request.base_url NOT LIKE '%://doi.org/10.48550/%'
AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%'
AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%'
AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%'
AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%'
AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%'
AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%'
AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%'
AND ingest_file_result.terminal_url NOT LIKE '%.archive.org%'
AND ingest_file_result.terminal_url NOT LIKE '%://archive.org%'
) t1
) TO '/srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.rows.json';
=> before ingest and arxiv.org DOI exclusion: COPY 3309091
=> COPY 3308914
Prep ingest requests (for post-crawl use):
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_$SNAPSHOT.json
=> 3.31M 0:02:22 [23.2k/s]
And actually dump seedlist(s):
cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.url.txt
cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.terminal_url.txt
cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.no_terminal_url.txt
cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.no_terminal_url.txt /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.terminal_url.txt | awk '{print "F+ " $1}' | shuf > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule
wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT*
15 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.no_terminal_url.txt
3308914 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.rows.json
3028879 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.terminal_url.txt
3038725 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.url.txt
Inject seedlist into crawler:
scp /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule $CRAWLVM:/tmp
ssh $CRAWLVM sudo -u heritrix cp /tmp/unpaywall_seedlist_$SNAPSHOT.schedule /0/ia-jobs/journal-crawls/$CRAWLNAME/action/
Top domains?
cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule | cut -f2 -d' ' | cut -f3 -d/ | sort -S 4G | uniq -c | sort -nr | head -n20
158497 www.scielo.br
144732 onlinelibrary.wiley.com
129349 www.researchsquare.com
94923 hal.archives-ouvertes.fr
69293 openresearchlibrary.org
64584 www.cell.com
60033 link.springer.com
50528 www.degruyter.com
49737 projecteuclid.org
45841 www.jstage.jst.go.jp
44819 www.mdpi.com
44325 ieeexplore.ieee.org
38091 dr.lib.iastate.edu
31030 www.nature.com
30300 discovery.ucl.ac.uk
27692 ntrs.nasa.gov
24215 orca.cardiff.ac.uk
23653 www.frontiersin.org
23474 pure.rug.nl
22660 www.sciencedirect.com
## Post-Crawl bulk ingest
# enqueue for bulk processing
cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_$SNAPSHOT.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc350.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
# done: 2022-07-06
## Post-Crawl, Post-Ingest Stats
SELECT ingest_file_result.status, COUNT(*)
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_file_result.ingest_type = ingest_request.ingest_type
AND ingest_file_result.base_url = ingest_request.base_url
WHERE
ingest_request.ingest_type = 'pdf'
AND ingest_request.link_source = 'unpaywall'
AND date(ingest_request.created) > '2022-04-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
success | 4784948 => +2,329,669 ~77%
redirect-loop | 485270 => + 288,153 ~10%
no-capture | 317598 => -3,012,457
terminal-bad-status | 267853 => + 185,235 ~ 6%
no-pdf-link | 118303 => + 85,257
blocked-cookie | 111373 => + 95,294
skip-url-blocklist | 19368
link-loop | 9091
wrong-mimetype | 7163
cdx-error | 2516
empty-blob | 1961
wayback-error | 1922
body-too-large | 509
petabox-error | 416
wayback-content-error | 341
bad-gzip-encoding | 281
| 253
null-body | 179
spn2-cdx-lookup-failure | 89
gateway-timeout | 73
(20 rows)
Groovy!
|
