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
|
New snapshot released 2021-07-02. Should be "boring" ingest and crawl.
## Transform and Load
# in sandcrawler pipenv on sandcrawler1-vm (svc506)
zcat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02T151134.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02.ingest_request.json
=> 32.2M 3:01:52 [2.95k/s]
cat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 32196260, 'insert-requests': 3325954, 'update-requests': 0})
=> JSON lines pushed: Counter({'total': 32196260, 'pushed': 32196260})
## 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'
-- 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_2021-07-02.rows.json';
=> COPY 3556146
# previous, 2020-10 run: COPY 4216339
# previous, 2021-07 run: COPY 3277484
Oops, should have run instead, with the date filter:
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'
AND date(ingest_request.created) > '2021-07-01'
AND (ingest_file_result.status IS NULL
OR ingest_file_result.status = 'no-capture')
) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.rows.json';
But didn't, so processed all instead.
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.ingest_request.json
=> 3.56M 0:01:59 [29.8k/s]
Enqueue the whole batch:
cat /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
=> done, on 2021-07-13
## 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) > '2021-07-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
no-capture | 1831827
success | 1343604
redirect-loop | 103999
terminal-bad-status | 19845
no-pdf-link | 17448
link-loop | 5027
wrong-mimetype | 2270
cdx-error | 523
body-too-large | 321
null-body | 298
wayback-content-error | 242
petabox-error | 155
gateway-timeout | 138
invalid-host-resolution | 120
wayback-error | 109
blocked-cookie | 9
timeout | 7
| 3
bad-redirect | 3
spn2-cdx-lookup-failure | 3
(20 rows)
## Dump Seedlist
Dump rows:
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) > '2021-07-01'
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 = 'spn2-cdx-lookup-failure'
)
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_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_2021-07-02.rows.json';
=> COPY 1743186
Prep ingest requests (for post-crawl use):
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-07-02.json
=> 1.74M 0:01:33 [18.6k/s]
And actually dump seedlist(s):
cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.url.txt
cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.terminal_url.txt
cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.no_terminal_url.txt
wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.*.txt
1 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.no_terminal_url.txt
1643963 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.terminal_url.txt
1644028 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.url.txt
3287992 total
Then run crawl (see `journal-crawls` git repo).
## Post-Crawl Bulk Ingest
cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-07-02.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
## Post-Ingest Stats
Overall status (unpaywall, all time):
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'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
Ingest stats broken down by publication stage:
SELECT ingest_request.release_stage, 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'
GROUP BY release_stage, status
ORDER BY release_stage, COUNT DESC
LIMIT 100;
Only the recent updates:
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) > '2021-07-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
In total, this iteration of unpaywall ingest resulted in:
- XXX raw ingest requests (new URLs total)
- XXX (YY%) of these had not been seen/crawled from any source yet
- XXX (YY%) success from new heritrix crawling
- XXX (YY%) total success (including crawled initially for other reasons; out of all new URLs including those not expected to be success)
|
