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It seems that many gold OA DOIs on were not ingesting simply because the HTML
url extraction was not working for a particular version of OJS.
Let's re-try all ~2.5 million of these in bulk mode and see how many are
'no-capture' vs. other errors, then possibly re-crawl a large number.
## Bulk Ingest
Dump ingest requests
./fatcat_ingest.py query 'is_oa:true preservation:none !arxiv_id:* !pmcid:* !publisher_type:big5 type:article-journal' | pv -l > /srv/fatcat/snapshots/oa_doi_20200915.ingest_request.json
Expecting 2569876 release objects in search queries
Counter({'elasticsearch_release': 2569880, 'estimate': 2569880, 'ingest_request': 2063034})
Enqueue
cat /srv/fatcat/snapshots/oa_doi_20200915.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Started at about:
Thu Sep 17 00:15:00 UTC 2020
2020-09-17T00:15:00Z
## 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.ingest_request_source = 'fatcat-ingest'
AND ingest_file_result.updated >= '2020-09-16'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 30;
status | count
-------------------------------------+--------
no-capture | 513462
success | 206042
no-pdf-link | 186779
terminal-bad-status | 40372
redirect-loop | 33103
cdx-error | 24078
link-loop | 13494
spn2-cdx-lookup-failure | 10247
gateway-timeout | 4407
wrong-mimetype | 3213
petabox-error | 866
null-body | 449
spn2-error | 217
wayback-error | 129
spn2-error:job-failed | 64
bad-redirect | 6
spn2-error:soft-time-limit-exceeded | 1
(17 rows)
This was only about half the requests. Try... broader?
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 = 'doi'
AND (ingest_request.ingest_request_source = 'fatcat-ingest'
OR ingest_request.ingest_request_source = 'fatcat-changelog')
AND ingest_file_result.updated >= '2020-09-15'
AND ingest_file_result.updated <= '2020-09-20'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 30;
status | count
-------------------------------------+--------
no-capture | 579952
success | 387325
no-pdf-link | 380406
terminal-bad-status | 63743
redirect-loop | 53893
cdx-error | 46024
spn2-cdx-lookup-failure | 28347
link-loop | 22573
gateway-timeout | 11686
wrong-mimetype | 6294
null-body | 3509
petabox-error | 2388
spn2-error | 1023
spn2-error:job-failed | 462
wayback-error | 347
spn2-error:soft-time-limit-exceeded | 20
bad-redirect | 11
(17 rows)
What top domains for those `no-pdf-link` (or similar)?
SELECT domain, status, COUNT((domain, status))
FROM (
SELECT
ingest_file_result.ingest_type,
ingest_file_result.status,
substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain
FROM ingest_file_result
LEFT JOIN ingest_request
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 = 'doi'
AND (ingest_request.ingest_request_source = 'fatcat-ingest'
OR ingest_request.ingest_request_source = 'fatcat-changelog')
AND ingest_file_result.updated >= '2020-09-15'
AND ingest_file_result.updated <= '2020-09-20'
) t1
WHERE t1.domain != ''
AND t1.status != 'success'
AND t1.status != 'no-capture'
GROUP BY domain, status
ORDER BY COUNT DESC
LIMIT 30;
domain | status | count
------------------------------+-------------------------+-------
zenodo.org | no-pdf-link | 56488
figshare.com | no-pdf-link | 55337
www.egms.de | redirect-loop | 22686
zenodo.org | terminal-bad-status | 22128
tandf.figshare.com | no-pdf-link | 20027
springernature.figshare.com | no-pdf-link | 17181
cairn.info | terminal-bad-status | 13836
www.persee.fr | terminal-bad-status | 7565
projecteuclid.org | link-loop | 7449
www.cairn.info | no-pdf-link | 6992
scialert.net | no-pdf-link | 6621
www.cairn.info | link-loop | 5870
utpjournals.press | no-pdf-link | 5772
journals.openedition.org | redirect-loop | 5464
www.egms.de | no-pdf-link | 5223
archaeologydataservice.ac.uk | no-pdf-link | 4881
rs.figshare.com | no-pdf-link | 4773
www.degruyter.com | spn2-cdx-lookup-failure | 4763
koreascience.or.kr | no-pdf-link | 4487
cancerres.aacrjournals.org | no-pdf-link | 4124
cms.math.ca | no-pdf-link | 3441
volcano.si.edu | no-pdf-link | 3424
www.mathnet.ru | no-pdf-link | 3229
tidsskriftet.no | no-pdf-link | 3012
journals.plos.org | no-pdf-link | 3005
tudigit.ulb.tu-darmstadt.de | no-pdf-link | 2796
www.cairn.info:80 | link-loop | 2647
hammer.figshare.com | no-pdf-link | 2627
www.psychosocial.com | no-pdf-link | 2457
osf.io | terminal-bad-status | 2388
(30 rows)
Will look at link extraction for:
- scialert.net
- utpjournals.press
- koreascience.or.kr
- cancerres.aacrjournals.org
- cms.math.ca
- volcano.si.edu
- www.mathnet.ru
- www.psychosocial.com
## Re-Ingest
Going to re-run ingest to handle `no-capture` cases, to extract the missing terminal URLs:
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 = 'doi'
AND (ingest_request.ingest_request_source = 'fatcat-ingest'
OR ingest_request.ingest_request_source = 'fatcat-changelog')
AND ingest_file_result.updated >= '2020-09-15'
AND ingest_file_result.updated <= '2020-09-20'
AND ingest_file_result.status = 'no-capture'
-- AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%'
) TO '/grande/snapshots/oa_doi_reingest_nocapture_20201012.rows.json';
=> COPY 579952
./scripts/ingestrequest_row2json.py /grande/snapshots/oa_doi_reingest_nocapture_20201012.rows.json | pv -l | shuf > /grande/snapshots/oa_doi_reingest_nocapture_20201012.ingest_request.json
=> 579k 0:00:22 [25.9k/s]
cat /grande/snapshots/oa_doi_reingest_nocapture_20201012.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
After that, will re-crawl somewhat broadly:
COPY (
SELECT row_to_json(r) FROM (
SELECT ingest_request.*, ingest_file_result.terminal_url as terminal_url
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 = 'doi'
AND (ingest_request.ingest_request_source = 'fatcat-ingest'
OR ingest_request.ingest_request_source = 'fatcat-changelog')
AND ((ingest_file_result.updated >= '2020-09-15' AND ingest_file_result.updated <= '2020-09-20')
OR (ingest_file_result.updated >= '2020-10-11'))
AND ingest_file_result.status != 'success'
) r
) TO '/grande/snapshots/oa_doi_reingest_recrawl_20201014.rows.json';
|
