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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)
Should 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
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
Resuming progress on this in early December 2020.
Filtered requests to re-crawl:
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.base_url = ingest_request.base_url
AND ingest_file_result.ingest_type = ingest_request.ingest_type
WHERE
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'
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 '%://web.archive.org/%'
AND ingest_request.base_url NOT LIKE '%://www.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 '%://web.archive.org/%'
AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%'
) t1
) TO '/grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json';
=> COPY 2352614
Prep ingest requests (for post-crawl use):
./scripts/ingestrequest_row2json.py /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | pv -l > /grande/snapshots/oa_doi_seedlist_2020-12-08.ingest_request.json
And actually dump seedlist(s):
cat /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | jq -r .base_url | rg '://' | sort -u -S 4G > /grande/snapshots/oa_doi_seedlist_2020-12-08.base_url.txt
cat /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | rg '://' | sort -u -S 4G > /grande/snapshots/oa_doi_seedlist_2020-12-08.no_capture_terminal_url.txt
wc -l /grande/snapshots/oa_doi_seedlist_2020-12-08.*.txt
2352614 /grande/snapshots/oa_doi_seedlist_2020-12-08.base_url.txt
481910 /grande/snapshots/oa_doi_seedlist_2020-12-08.no_capture_terminal_url.txt
Top DOI prefixes (same old usual suspects):
cat /grande/snapshots/oa_doi_seedlist_2020-12-08.*url.txt | rg ^http | rg "://doi.org/" | cut -f4 -d/ | sort | uniq -c | sort -nr | head -n20
353695 10.5281 zenodo.org
121888 10.6084 figshare.org
115093 10.3917 cairn.info
113252 10.3406 persee.fr
95414 10.1515 degruyter.com
90448 10.4324 taylorfrancis.com
83927 10.1016 elsevier
60303 10.1109 IEEE
48490 10.4000 openedition.org
28498 10.3205 egms.de
23433 10.1163 brill.com
23276 10.17615 cdr.lib.unc.edu
21386 10.1093 oup.com
20783 10.3138 utpjournals.press
19987 10.1201 tandfonline.com
17916 10.34847 cocoon.huma-num.fr
16970 10.1002 wiley.com
15958 10.1097 lww.com (and others?)
15835 10.1017 cambridge.org
15466 10.24355 publikationsserver.tu-braunschweig.de (IR)
Top domains (not doi.org):
cat /grande/snapshots/oa_doi_seedlist_2020-12-08.*url.txt | rg ^http | rg -v "://doi.org/" | cut -f3 -d/ | sort | uniq -c | sort -nr | head -n20
104148 zenodo.org
85245 www.persee.fr
52931 www.cairn.info
4791 www.jstage.jst.go.jp
4411 archive.monthlyreview.org
4129 osf.io
2841 www.indianjournals.com
2746 www.impan.pl
2620 platform.almanhal.com
2019 www.nomos-elibrary.de
1209 dergipark.org.tr
1027 pubs.geoscienceworld.org
973 www.pdcnet.org
923 www.hanspub.org
914 www.repository.cam.ac.uk
863 mediarep.org
812 www.cartographicperspectives.org
687 www.degruyter.com
578 192.168.7.24
566 journals.eco-vector.com
TODO: infer `publisher_type` and platform from DOI prefix in more cases
## Re-Ingest
Crawl has completed. Starting this bulk ingest on 2020-12-31; roughly 2.3
million requests. Note these are all `pdf` requests, but crawl was done in an
HTML-friendly way, so should be able to do domain/journal-specific HTML ingests
in the future.
cat /grande/snapshots/oa_doi_seedlist_2020-12-08.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Stats, for this ingest period (fuzzy; will have some daily ingest stuff):
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 >= '2020-12-28'
AND ingest_request.created <= '2020-12-09'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 30;
status | count
-----------------------+--------
no-pdf-link | 962714
success | 539305
no-capture | 306590
redirect-loop | 192149
link-loop | 184797
terminal-bad-status | 141721
wrong-mimetype | 10362
null-body | 10277
skip-url-blocklist | 1985
wayback-content-error | 1300
cdx-error | 869
petabox-error | 160
bad-redirect | 72
wayback-error | 46
bad-gzip-encoding | 7
timeout | 1
max-hops-exceeded | 1
(17 rows)
|
