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|
Using 2021-06-07 upstream MAG snapshot to run a crawl and do some re-ingest.
Also want to re-ingest some old/failed ingests, now that pipeline/code has
improved.
Ran munging from `scratch:ingest/mag` notes first. Yielded 22.5M PDF URLs.
## Persist Ingest Requests
zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | head -n1000 | pv -l | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 1000, 'insert-requests': 276, 'update-requests': 0})
=> JSON lines pushed: Counter({'total': 1000, 'pushed': 1000})
zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | pv -l | ./persist_tool.py ingest-request -
=> 22.5M 0:46:00 [8.16k/s]
=> Worker: Counter({'total': 22527585, 'insert-requests': 8686315, 'update-requests': 0})
=> JSON lines pushed: Counter({'total': 22527585, 'pushed': 22527585})
Roughly 8.6 million new URLs
## Pre-Crawl Status Counts
Status of combined old and new requests, with some large domains removed:
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 = 'mag'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
-- AND ingest_request.created > '2021-06-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------+----------
success | 26123975
| 6664846
no-pdf-link | 1859908
redirect-loop | 1532405
no-capture | 1199126
link-loop | 1157010
terminal-bad-status | 832362
gateway-timeout | 202158
spn2-cdx-lookup-failure | 81406
wrong-mimetype | 69087
invalid-host-resolution | 37262
wayback-error | 21340
petabox-error | 11237
null-body | 9414
wayback-content-error | 2199
cdx-error | 1893
spn2-error | 1741
spn2-error:job-failed | 971
blocked-cookie | 902
spn2-error:invalid-url-syntax | 336
(20 rows)
And just the new URLs (note that domain filter shouldn't be required, but
keeping for consistency):
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 = 'mag'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
AND ingest_request.created > '2021-06-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
| 6664780
success | 1957844
redirect-loop | 23357
terminal-bad-status | 9385
no-pdf-link | 8315
no-capture | 6892
link-loop | 4517
wrong-mimetype | 3864
cdx-error | 1749
blocked-cookie | 842
null-body | 747
wayback-error | 688
wayback-content-error | 570
gateway-timeout | 367
petabox-error | 340
spn2-cdx-lookup-failure | 150
read-timeout | 122
not-found | 119
invalid-host-resolution | 63
spn2-error | 23
(20 rows)
## Dump Initial Bulk Ingest Requests
Note that this is all-time, not just recent, and will re-process a lot of
"no-pdf-link":
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 = 'mag'
AND (
ingest_file_result.status IS NULL
OR ingest_file_result.status = 'no-pdf-link'
OR ingest_file_result.status = 'cdx-error'
)
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json';
=> COPY 8526647
Transform to ingest requests:
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.ingest_request.json
=> 8.53M 0:03:40
Enqueue the whole batch:
cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.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
Updated stats after running initial 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 = 'mag'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
AND ingest_request.created > '2021-06-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
success | 5184994
no-capture | 3284416
redirect-loop | 98685
terminal-bad-status | 28733
link-loop | 28518
blocked-cookie | 22338
no-pdf-link | 19073
wrong-mimetype | 9122
null-body | 2793
wayback-error | 2128
wayback-content-error | 1233
cdx-error | 1198
petabox-error | 617
gateway-timeout | 395
not-found | 130
read-timeout | 128
| 111
invalid-host-resolution | 63
spn2-cdx-lookup-failure | 24
spn2-error | 20
(20 rows)
## Generate Seedlist
For crawling, do a similar (but not identical) dump:
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 ingest_request.link_source = 'mag'
AND (
ingest_file_result.status IS NULL
OR 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 = 'wayback-content-error'
OR ingest_file_result.status = 'petabox-error'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
) t1
) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json';
=> COPY 4599519
Prep ingest requests (for post-crawl use):
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | pv -l > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.ingest_request.json
=> 4.60M 0:02:55 [26.2k/s]
And actually dump seedlist(s):
cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt
cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt
cat /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt
=> DONE
wc -l /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.*.txt
4593238 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt
4632911 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt
3294710 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt
## Post-Crawl Bulk Re-Ingest
Got about 1.8 million new PDFs from crawl, and a sizable fraction of dupes (by
hash, URL agnostic).
Enqueue for buik re-ingest:
cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
=> Thu 19 Aug 2021 09:10:59 PM UTC
## Post-Ingest Stats
Just the new stuff (compare against above for delta):
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 = 'mag'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
AND ingest_request.created > '2021-06-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------+---------
success | 7748241 89.2%
no-capture | 429688 4.9%
redirect-loop | 172831 2.0%
terminal-bad-status | 94029 1.1%
no-pdf-link | 86437 1.0%
blocked-cookie | 67903 0.8%
link-loop | 50622
wrong-mimetype | 21064
null-body | 6650
cdx-error | 3313
wayback-error | 2630
gateway-timeout | 399
petabox-error | 268
wayback-content-error | 170
not-found | 130
read-timeout | 128
| 109
invalid-host-resolution | 63
bad-redirect | 39
spn2-error | 20
(20 rows)
New success due to crawl (new batch only): 7748241 - 1957844 = 5,790,397
Overall success of new batch: 7748241. / 8686315 = 89.2%
And combined (old and new) status again:
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 = 'mag'
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 '%researchgate.net%'
AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
AND ingest_request.base_url NOT LIKE '%link.springer.com%'
AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
-- AND ingest_request.created > '2021-06-01'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+----------
success | 31990062
redirect-loop | 1704717
no-capture | 1263462
link-loop | 1218280
blocked-cookie | 1213838
no-pdf-link | 1096664
terminal-bad-status | 960070
gateway-timeout | 202190
wrong-mimetype | 86557
invalid-host-resolution | 37262
null-body | 15443
wayback-error | 12839
cdx-error | 4047
spn2-error | 1731
spn2-error:job-failed | 962
petabox-error | 463
wayback-content-error | 379
spn2-error:invalid-url-syntax | 336
spn2-error:soft-time-limit-exceeded | 203
| 175
(20 rows)
New success total: 31990062 - 26123975 = 5,866,087
A full 1,263,462 no-capture that could be attempted... though many of those may
be excluded for a specific reason.
|
