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|
Starting another paper fulltext patch crawl, targetting recent OA content which
has failed to ingest, and platforms (arxiv, etc).
Specifically:
- "daily" changelog ingest requests from all time, which failed with various status codes
- pdf no-capture
- SPN errors
- terminal-bad-status with 5xx, 429
- gateway-timeout
- html no-capture
- html-resource-no-capture
Most of these are dumped in a single complex query (below),
TODO: html-resource-no-capture (from error message? or do SPN requests separately?)
## Initial 'no-capture' Seedlist
Dump terminal URLs (will do ingest requests later, using similar command):
COPY (
SELECT ingest_file_result.terminal_url
-- 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'
OR ingest_request.ingest_type = 'html'
)
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 = 'wayback-content-error'
OR ingest_file_result.status = 'petabox-error'
OR ingest_file_result.status = 'spn2-cdx-lookup-failure'
OR ingest_file_result.status = 'gateway-timeout'
OR (
ingest_file_result.status = 'terminal-bad-status'
AND (
ingest_file_result.terminal_status_code = 429
OR ingest_file_result.terminal_status_code = 500
OR ingest_file_result.terminal_status_code = 502
OR ingest_file_result.terminal_status_code = 503
)
)
)
AND (
ingest_request.link_source = 'oai'
OR ingest_request.link_source = 'doi'
OR ingest_request.link_source = 'arxiv'
OR ingest_request.link_source = 'doaj'
OR ingest_request.link_source = 'unpaywall'
OR ingest_request.link_source = 'pmc'
)
AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%'
AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repec:%'
AND ingest_request.link_source_id NOT LIKE 'oai:n/a:%'
AND ingest_request.link_source_id NOT LIKE 'oai:quod.lib.umich.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:americanae.aecid.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:www.irgrid.ac.cn:%'
AND ingest_request.link_source_id NOT LIKE 'oai:espace.library.uq.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:edoc.mpg.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bibliotecadigital.jcyl.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repository.erciyes.edu.tr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:krm.or.kr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%'
AND ingest_file_result.terminal_url NOT LIKE '%mdz-nbn-resolving.de%'
AND ingest_file_result.terminal_url NOT LIKE '%edoc.mpg.de%'
AND ingest_file_result.terminal_url NOT LIKE '%doaj.org%'
AND ingest_file_result.terminal_url NOT LIKE '%orcid.org%'
AND ingest_file_result.terminal_url NOT LIKE '%gateway.isiknowledge.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%europmc.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%arxiv.org%'
-- AND ingest_file_result.terminal_url NOT LIKE 'https://doi.org/10.%'
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 '%researchgate.net%'
AND ingest_file_result.terminal_url NOT LIKE '%muse.jhu.edu%'
AND ingest_file_result.terminal_url NOT LIKE '%omicsonline.org%'
AND ingest_file_result.terminal_url NOT LIKE '%link.springer.com%'
AND ingest_file_result.terminal_url NOT LIKE '%ieeexplore.ieee.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%zenodo.org%'
AND ingest_file_result.terminal_url NOT LIKE '%t2r2.star.titech.ac.jp%'
AND ingest_file_result.terminal_url NOT LIKE '%www.google.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%figshare.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%springernature.figshare.com%'
-- ) TO '/srv/sandcrawler/tasks/patch_ingest_request_2022-01-12.rows.json';
) TO '/srv/sandcrawler/tasks/patch_terminal_url.2022-01-12.txt';
=> COPY 6389683
TODO: filter out archive.org/www.archive.org
cat patch_terminal_url.2022-01-12.txt \
| rg -v www.archive.org \
| rg '://' \
| rg -v '://10\.' \
| rg -v '://172\.' \
| rg -i '^http' \
| sort -u -S 4G \
| pv -l \
> patch_terminal_url.2022-01-12.uniq.txt
=> 5.73M 0:00:47 [ 120k/s]
# note: tweaks and re-ran the above after inspecting this output
cut -f3 -d/ patch_terminal_url.2022-01-12.uniq.txt | sort | uniq -c | sort -nr | head -n25
799045 doi.org
317557 linkinghub.elsevier.com
211091 arxiv.org
204334 iopscience.iop.org
139758 dialnet.unirioja.es
130331 www.scielo.br
124626 www.persee.fr
85764 digitalrepository.unm.edu
83913 www.mdpi.com
79662 www.degruyter.com
75703 www.e-periodica.ch
72206 dx.doi.org
69068 escholarship.org
67848 idus.us.es
57907 zenodo.org
56624 ir.opt.ac.cn
54983 projecteuclid.org
52226 rep.bntu.by
48376 osf.io
48009 pubs.rsc.org
46947 publikationen.ub.uni-frankfurt.de
45564 www.research-collection.ethz.ch
45153 dk.um.si
43313 www.ssoar.info
40543 scholarworks.umt.edu
TODO: cleanup ingest request table in sandcrawler-db:
- remove filtered OAI-PMH prefixes
- remove any invalid `base_url` (?)
## More Seedlist (2022-02-08)
COPY (
SELECT ingest_file_result.terminal_url
-- 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'
OR ingest_request.ingest_type = 'html'
)
AND ingest_file_result.updated >= '2022-01-12'
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 = 'wayback-content-error'
OR ingest_file_result.status = 'petabox-error'
OR ingest_file_result.status = 'spn2-cdx-lookup-failure'
OR ingest_file_result.status = 'gateway-timeout'
OR (
ingest_file_result.status = 'terminal-bad-status'
AND (
ingest_file_result.terminal_status_code = 429
OR ingest_file_result.terminal_status_code = 500
OR ingest_file_result.terminal_status_code = 502
OR ingest_file_result.terminal_status_code = 503
)
)
)
AND (
ingest_request.link_source = 'oai'
OR ingest_request.link_source = 'doi'
OR ingest_request.link_source = 'arxiv'
OR ingest_request.link_source = 'doaj'
OR ingest_request.link_source = 'unpaywall'
OR ingest_request.link_source = 'pmc'
)
AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%'
AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repec:%'
AND ingest_request.link_source_id NOT LIKE 'oai:n/a:%'
AND ingest_request.link_source_id NOT LIKE 'oai:quod.lib.umich.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:americanae.aecid.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:www.irgrid.ac.cn:%'
AND ingest_request.link_source_id NOT LIKE 'oai:espace.library.uq.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:edoc.mpg.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bibliotecadigital.jcyl.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repository.erciyes.edu.tr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:krm.or.kr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%'
AND ingest_file_result.terminal_url NOT LIKE '%mdz-nbn-resolving.de%'
AND ingest_file_result.terminal_url NOT LIKE '%edoc.mpg.de%'
AND ingest_file_result.terminal_url NOT LIKE '%doaj.org%'
AND ingest_file_result.terminal_url NOT LIKE '%orcid.org%'
AND ingest_file_result.terminal_url NOT LIKE '%gateway.isiknowledge.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%europmc.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%arxiv.org%'
-- AND ingest_file_result.terminal_url NOT LIKE 'https://doi.org/10.%'
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 '%researchgate.net%'
AND ingest_file_result.terminal_url NOT LIKE '%muse.jhu.edu%'
AND ingest_file_result.terminal_url NOT LIKE '%omicsonline.org%'
AND ingest_file_result.terminal_url NOT LIKE '%link.springer.com%'
AND ingest_file_result.terminal_url NOT LIKE '%ieeexplore.ieee.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%zenodo.org%'
AND ingest_file_result.terminal_url NOT LIKE '%t2r2.star.titech.ac.jp%'
AND ingest_file_result.terminal_url NOT LIKE '%www.google.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%figshare.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%springernature.figshare.com%'
AND ingest_file_result.terminal_url NOT LIKE '%www.archive.org%'
-- ) TO '/srv/sandcrawler/tasks/patch_ingest_request_2022-02-08.rows.json';
) TO '/srv/sandcrawler/tasks/patch_terminal_url.2022-02-08.txt';
=> COPY 444764
cat patch_terminal_url.2022-02-08.txt \
| rg -v www.archive.org \
| rg '://' \
| rg -v '://10\.' \
| rg -v '://172\.' \
| rg -i '^http' \
| sort -u -S 4G \
| pv -l \
> patch_terminal_url.2022-02-08.uniq.txt
=> 426k 0:00:04 [ 103k/s]
cut -f3 -d/ patch_terminal_url.2022-02-08.uniq.txt | sort | uniq -c | sort -nr | head -n25
60123 www.degruyter.com
59314 arxiv.org
43674 zenodo.org
17771 doi.org
9501 linkinghub.elsevier.com
9379 www.mdpi.com
5691 opendata.uni-halle.de
5578 scholarlypublishingcollective.org
5451 era.library.ualberta.ca
4982 www.cairn.info
4306 www.taylorfrancis.com
4189 papers.ssrn.com
4157 apps.crossref.org
4089 www.sciencedirect.com
4033 mdpi-res.com
3763 dlc.mpg.de
3408 osf.io
2603 www.frontiersin.org
2594 watermark.silverchair.com
2569 journals.lww.com
1787 underline.io
1680 archiviostorico.fondazione1563.it
1658 www.jstage.jst.go.jp
1611 cyberleninka.ru
1535 www.schoeningh.de
cat patch_terminal_url.2022-02-08.txt | awk '{print "F+ " $1}' > patch_terminal_url.2022-02-08.schedule
=> Done
Copied to crawler svc206 and added to frontier.
## Bulk Ingest Requests (2022-02-28)
Note that we are skipping OAI-PMH here, because we just did a separate ingest
for those.
This is going to dump many duplicate lines (same `base_url`, multiple
requests), but that is fine. Expecting something like 7 million rows.
COPY (
-- SELECT ingest_file_result.terminal_url
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'
OR ingest_request.ingest_type = 'html'
)
AND ingest_file_result.updated <= '2022-02-08'
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 = 'wayback-content-error'
OR ingest_file_result.status = 'petabox-error'
OR ingest_file_result.status = 'spn2-cdx-lookup-failure'
OR ingest_file_result.status = 'gateway-timeout'
OR (
ingest_file_result.status = 'terminal-bad-status'
AND (
ingest_file_result.terminal_status_code = 429
OR ingest_file_result.terminal_status_code = 500
OR ingest_file_result.terminal_status_code = 502
OR ingest_file_result.terminal_status_code = 503
)
)
)
AND (
-- ingest_request.link_source = 'oai'
ingest_request.link_source = 'doi'
OR ingest_request.link_source = 'arxiv'
OR ingest_request.link_source = 'doaj'
OR ingest_request.link_source = 'unpaywall'
OR ingest_request.link_source = 'pmc'
)
AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%'
AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repec:%'
AND ingest_request.link_source_id NOT LIKE 'oai:n/a:%'
AND ingest_request.link_source_id NOT LIKE 'oai:quod.lib.umich.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:americanae.aecid.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:www.irgrid.ac.cn:%'
AND ingest_request.link_source_id NOT LIKE 'oai:espace.library.uq.edu:%'
AND ingest_request.link_source_id NOT LIKE 'oai:edoc.mpg.de:%'
AND ingest_request.link_source_id NOT LIKE 'oai:bibliotecadigital.jcyl.es:%'
AND ingest_request.link_source_id NOT LIKE 'oai:repository.erciyes.edu.tr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:krm.or.kr:%'
AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%'
AND ingest_file_result.terminal_url NOT LIKE '%mdz-nbn-resolving.de%'
AND ingest_file_result.terminal_url NOT LIKE '%edoc.mpg.de%'
AND ingest_file_result.terminal_url NOT LIKE '%doaj.org%'
AND ingest_file_result.terminal_url NOT LIKE '%orcid.org%'
AND ingest_file_result.terminal_url NOT LIKE '%gateway.isiknowledge.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%europmc.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%arxiv.org%'
-- AND ingest_file_result.terminal_url NOT LIKE 'https://doi.org/10.%'
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 '%researchgate.net%'
AND ingest_file_result.terminal_url NOT LIKE '%muse.jhu.edu%'
AND ingest_file_result.terminal_url NOT LIKE '%omicsonline.org%'
AND ingest_file_result.terminal_url NOT LIKE '%link.springer.com%'
AND ingest_file_result.terminal_url NOT LIKE '%ieeexplore.ieee.org%'
-- AND ingest_file_result.terminal_url NOT LIKE '%zenodo.org%'
AND ingest_file_result.terminal_url NOT LIKE '%t2r2.star.titech.ac.jp%'
AND ingest_file_result.terminal_url NOT LIKE '%www.google.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%figshare.com%'
-- AND ingest_file_result.terminal_url NOT LIKE '%springernature.figshare.com%'
AND ingest_file_result.terminal_url NOT LIKE '%www.archive.org%'
) TO '/srv/sandcrawler/tasks/patch_ingest_request_2022-02-28.rows.json';
# COPY 3053219
./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/patch_ingest_request_2022-02-28.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/patch_ingest_request_2022-02-28.ingest_request.json
=> DONE
cat /srv/sandcrawler/tasks/patch_ingest_request_2022-02-28.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
|
