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| -rw-r--r-- | notes/ingest/2021-04_unpaywall.md | 368 |
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diff --git a/notes/ingest/2021-04_unpaywall.md b/notes/ingest/2021-04_unpaywall.md new file mode 100644 index 0000000..d7643f4 --- /dev/null +++ b/notes/ingest/2021-04_unpaywall.md @@ -0,0 +1,368 @@ + +New snapshot released 2021-02-18, finally getting around to a crawl two months +later. + +Intend to do same style of crawl as in the past. One change is that +sandcrawler-db has moved to a focal VM. + + +## Transform and Load + + # in sandcrawler pipenv on sandcrawler1-vm (svc506) + zcat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18T160139.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18.ingest_request.json + => 30.0M 3:14:59 [2.57k/s] + + cat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 30027007, 'insert-requests': 2703999, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 30027007, 'pushed': 30027007}) + +## Dump new URLs, Transform, Bulk Ingest + + 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 = 'unpaywall' + -- AND date(ingest_request.created) > '2021-01-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.rows.json'; + => COPY 3277484 + + # previous, 2020-10 run: COPY 4216339 + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.ingest_request.json + => 3.28M 0:01:42 [32.1k/s] + +Enqueue the whole batch: + + cat /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + +## Check Pre-Crawl Status + + 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 = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------+---------- + success | 26385866 + no-pdf-link | 2132565 + no-capture | 2092111 + redirect-loop | 1732543 + terminal-bad-status | 1504555 + wayback-content-error | 357345 + wrong-mimetype | 126070 + link-loop | 76808 + cdx-error | 22756 + null-body | 22066 + wayback-error | 13768 + gateway-timeout | 3804 + petabox-error | 3608 + spn2-cdx-lookup-failure | 1225 + redirects-exceeded | 892 + invalid-host-resolution | 505 + bad-redirect | 151 + spn2-error | 108 + spn2-error:job-failed | 91 + bad-gzip-encoding | 27 + (20 rows) + +Only the recent 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 = 'unpaywall' + AND date(ingest_request.created) > '2021-01-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 1348623 + no-capture | 1231582 + redirect-loop | 45622 + no-pdf-link | 37312 + terminal-bad-status | 24162 + wrong-mimetype | 6684 + link-loop | 5757 + null-body | 1288 + wayback-content-error | 1123 + cdx-error | 831 + petabox-error | 697 + wayback-error | 185 + invalid-host-resolution | 41 + gateway-timeout | 29 + blocked-cookie | 22 + bad-gzip-encoding | 20 + spn2-cdx-lookup-failure | 7 + bad-redirect | 4 + timeout | 3 + redirects-exceeded | 3 + (20 rows) + +## Dump Seedlist + +Dump rows: + + 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 = 'unpaywall' + 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 = 'gateway-timeout' + 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 '%.archive.org%' + AND ingest_request.base_url NOT LIKE '%://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 '%://archive.org%' + ) t1 + ) TO '/srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json'; + => 2020-10: 2,936,404 + => 2021-04: 1,805,192 + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-02-18.json + => 1.81M 0:01:27 [20.6k/s] + +And actually dump seedlist(s): + + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.terminal_url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.no_terminal_url.txt + + wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.*.txt + 6 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.no_terminal_url.txt + 1668524 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.terminal_url.txt + 1685717 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.url.txt + +## Post-Crawl Bulk Ingest + + cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-02-18.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => 1,804,211 consumer group lag + +## Post-Ingest Stats + +Overall status (unpaywall, all time): + + 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 = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + success | 27242251 + no-pdf-link | 2746237 + redirect-loop | 1821132 + terminal-bad-status | 1553441 + no-capture | 478559 + wayback-content-error | 357390 + wrong-mimetype | 127365 + link-loop | 79389 + cdx-error | 23170 + null-body | 23169 + wayback-error | 13704 + gateway-timeout | 3803 + petabox-error | 3642 + redirects-exceeded | 1427 + spn2-cdx-lookup-failure | 1214 + invalid-host-resolution | 505 + bad-redirect | 153 + spn2-error | 107 + spn2-error:job-failed | 91 + body-too-large | 84 + (20 rows) + +Ingest stats broken down by publication stage: + + SELECT ingest_request.release_stage, 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 = 'unpaywall' + GROUP BY release_stage, status + ORDER BY release_stage, COUNT DESC + LIMIT 100; + + release_stage | status | count + ---------------+-------------------------------------+---------- + accepted | success | 1213335 + accepted | no-pdf-link | 29292 + accepted | redirect-loop | 12769 + accepted | terminal-bad-status | 11264 + accepted | no-capture | 10187 + accepted | cdx-error | 1015 + accepted | wayback-content-error | 757 + accepted | wrong-mimetype | 501 + accepted | link-loop | 407 + accepted | wayback-error | 207 + accepted | petabox-error | 189 + accepted | redirects-exceeded | 125 + accepted | null-body | 34 + accepted | spn2-cdx-lookup-failure | 5 + accepted | gateway-timeout | 4 + accepted | blocked-cookie | 2 + accepted | bad-redirect | 1 + accepted | body-too-large | 1 + published | success | 20196774 + published | no-pdf-link | 2647969 + published | redirect-loop | 1477558 + published | terminal-bad-status | 1320013 + published | wayback-content-error | 351931 + published | no-capture | 297603 + published | wrong-mimetype | 115440 + published | link-loop | 76431 + published | cdx-error | 18125 + published | null-body | 17559 + published | wayback-error | 10466 + published | petabox-error | 2684 + published | gateway-timeout | 1979 + published | redirects-exceeded | 947 + published | spn2-cdx-lookup-failure | 877 + published | invalid-host-resolution | 457 + published | bad-redirect | 120 + published | spn2-error:job-failed | 77 + published | spn2-error | 70 + published | body-too-large | 39 + published | bad-gzip-encoding | 24 + published | timeout | 24 + published | blocked-cookie | 23 + published | spn2-error:soft-time-limit-exceeded | 4 + published | | 2 + published | pending | 1 + published | spn2-error:pending | 1 + published | too-many-redirects | 1 + submitted | success | 5832117 + submitted | redirect-loop | 330785 + submitted | terminal-bad-status | 222152 + submitted | no-capture | 170766 + submitted | no-pdf-link | 68934 + submitted | wrong-mimetype | 11424 + submitted | null-body | 5576 + submitted | wayback-content-error | 4702 + submitted | cdx-error | 4030 + submitted | wayback-error | 3031 + submitted | link-loop | 2551 + submitted | gateway-timeout | 1820 + submitted | petabox-error | 769 + submitted | redirects-exceeded | 355 + submitted | spn2-cdx-lookup-failure | 332 + submitted | invalid-host-resolution | 48 + submitted | body-too-large | 44 + submitted | spn2-error | 37 + submitted | bad-redirect | 32 + submitted | spn2-error:job-failed | 14 + submitted | | 13 + submitted | spn2-error:soft-time-limit-exceeded | 5 + submitted | timeout | 4 + submitted | bad-gzip-encoding | 3 + submitted | skip-url-blocklist | 1 + | no-pdf-link | 42 + | success | 25 + | redirect-loop | 20 + | terminal-bad-status | 12 + | no-capture | 3 + (76 rows) + + +Only the recent updates: + + 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 = 'unpaywall' + AND date(ingest_request.created) > '2021-04-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 2192376 + no-capture | 152183 + no-pdf-link | 144174 + redirect-loop | 125988 + terminal-bad-status | 67307 + link-loop | 8292 + wrong-mimetype | 7942 + null-body | 2270 + cdx-error | 1223 + wayback-content-error | 1147 + petabox-error | 728 + wayback-error | 155 + body-too-large | 82 + invalid-host-resolution | 41 + gateway-timeout | 28 + blocked-cookie | 22 + bad-gzip-encoding | 20 + timeout | 7 + bad-redirect | 6 + redirects-exceeded | 4 + (20 rows) + +In total, this iteration of unpaywall ingest resulted in: + +- 2,703,999 raw ingest requests (new URLs total) +- 1,231,582 (45.5%) of these had not been seen/crawled from any source yet +- 843,753 (31.2%) success from new heritrix crawling +- 2,192,376 (81.1%) total success (including crawled initially for other reasons; out of all new URLs including those not expected to be success) |