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authorBryan Newbold <bnewbold@archive.org>2020-10-17 17:12:14 -0700
committerBryan Newbold <bnewbold@archive.org>2020-10-17 17:12:14 -0700
commit0c924003291ea1a41cf0543463d2b9ce43d123fd (patch)
treecb2b172861e0b6d724e8b56987b0c108f5156a92
parent1695c1bcd0d084a2004ce24bc01fd4515b49c06d (diff)
downloadsandcrawler-0c924003291ea1a41cf0543463d2b9ce43d123fd.tar.gz
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OA DOIs: partial notes
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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';
+