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diff --git a/notes/ingest/2021-09-03_patch_crawl.md b/notes/ingest/2021-09-03_patch_crawl.md new file mode 100644 index 0000000..f63e524 --- /dev/null +++ b/notes/ingest/2021-09-03_patch_crawl.md @@ -0,0 +1,488 @@ + +Going to run a combined crawl for `no-capture`, `no-pdf-link` and similar URL +statuses. + +As a reminder, significant refactor of PDF URL extraction happened around +Oct/Nov 2020, so things not re-ingested since then should be retried. + +1. first bulk re-process `no-pdf-link` statuses from OAI-PMH crawl past OA DOI past crawls +2. then heritrix crawl of old URLs from all sources (see status codes below) +3. bulk ingest specific sources and statuses (see below) + +Status codes to crawl, with potentially split separate batches: + + no-capture + IA errors + cdx-error + wayback-error + wayback-content-error + petabox-error + spn2-cdx-lookup-failure + gateway-timeout + +Then, bulk ingest from these sources matching the above patterns, in this order: + +- OA DOI (fatcat-ingest or fatcat-changelog source; will result in import) +- unpaywall (will result in import) +- OAI-PMH +- MAG + +Current combined domain skip list (SQL filter syntax), for which we don't want +to bother retrying: + + '%journals.sagepub.com%' + '%pubs.acs.org%' + '%ahajournals.org%' + '%www.journal.csj.jp%' + '%aip.scitation.org%' + '%academic.oup.com%' + '%tandfonline.com%' + '%://orcid.org/%' + '%://doaj.org/%' + '%://archive.org/%' + '%://web.archive.org/%' + '%://www.archive.org/%' + +## DOI Ingest Status (2021-09-08) + +Recently did some analysis of OAI-PMH overall status, so can re-do comparisons +there easily. What about overall DOI ingest? Would like counts so we can +compare before/after. + + 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' + ) + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------+---------- + no-pdf-link | 10516478 + success | 5690862 + redirect-loop | 1827192 + no-capture | 1215179 + terminal-bad-status | 650104 + link-loop | 610251 + blocked-cookie | 353681 + gateway-timeout | 341319 + too-many-redirects | 307895 + forbidden | 306710 + spn2-cdx-lookup-failure | 282955 + not-found | 273667 + cdx-error | 269082 + skip-url-blocklist | 265689 + spn2-error | 87759 + wrong-mimetype | 68993 + spn2-error:too-many-redirects | 58064 + wayback-error | 54152 + spn2-wayback-error | 51752 + remote-server-error | 45683 + (20 rows) + +## `no-pdf-link` re-try bulk ingest + +Specifically for past OAI-PMH and OA DOI crawls. + +What are top terminal domains that would be retried? So that we can filter out +large ones we don't want to bother retrying. + + SELECT domain, COUNT(domain) + FROM ( + SELECT + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + 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_file_result.status = 'no-pdf-link' + AND ( + ingest_request.link_source = 'oai' + OR ( + ingest_request.link_source = 'doi' + AND ( + ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog' + ) + ) + ) + + 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.%' + ) t1 + WHERE t1.domain != '' + GROUP BY domain + ORDER BY COUNT DESC + LIMIT 40; + + domain | count + ---------------------------------------+-------- + ssl.fao.org | 862277 + www.e-periodica.ch | 828110 + zenodo.org | 686701 + plutof.ut.ee | 685440 + www.gbif.org | 669727 + dlc.library.columbia.edu | 536018 + figshare.com | 383181 + juser.fz-juelich.de | 351519 + statisticaldatasets.data-planet.com | 320415 + espace.library.uq.edu.au | 310767 + invenio.nusl.cz | 309731 + doi.pangaea.de | 306311 + igi.indrastra.com | 297872 + bib-pubdb1.desy.de | 273565 + t2r2.star.titech.ac.jp | 271907 + digi.ub.uni-heidelberg.de | 265519 + www.sciencedirect.com | 263847 + publikationen.bibliothek.kit.edu | 229960 + www.plate-archive.org | 209231 + www.degruyter.com | 189776 + spectradspace.lib.imperial.ac.uk:8443 | 187086 + hal.archives-ouvertes.fr | 185513 + open.library.ubc.ca | 172821 + lup.lub.lu.se | 170063 + books.openedition.org | 169501 + orbi.uliege.be | 161443 + freidok.uni-freiburg.de | 150310 + library.wur.nl | 124318 + digital.library.pitt.edu | 116406 + www.research.manchester.ac.uk | 115869 + www.bibliotecavirtualdeandalucia.es | 114527 + repository.tue.nl | 112157 + www.google.com | 111569 + easy.dans.knaw.nl | 109608 + springernature.figshare.com | 108597 + nbn-resolving.org | 107544 + scholarbank.nus.edu.sg | 107299 + bibliotecavirtualdefensa.es | 105501 + biblio.ugent.be | 100854 + ruj.uj.edu.pl | 99500 + (40 rows) + +For a number of these domains, we do not expect any PDFs to be found, but are +going to re-ingest anyways so they get marked as 'blocked-*' in result table: + +- ssl.fao.org +- plutof.ut.ee +- www.gbif.org + +But some we are just going to skip anyways, because there *could* be PDFs, but +probably *aren't*: + +- zenodo.org +- t2r2.star.titech.ac.jp +- www.google.com +- figshare.com +- springernature.figshare.com + +Dump ingest requests: + + 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_file_result.status = 'no-pdf-link' + AND ( + ingest_request.link_source = 'oai' + OR ( + ingest_request.link_source = 'doi' + AND ( + ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog' + ) + ) + ) + + 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_2021-09-08.rows.json'; + => COPY 18040676 + +Transform and start ingest: + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/patch_ingest_request_2021-09-08.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/patch_ingest_request_2021-09-08.ingest_request.json + => 18.0M 0:06:45 [44.5k/s] + + cat /srv/sandcrawler/tasks/patch_ingest_request_2021-09-08.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + => DONE + +## Progress Check + +OAI-PMH query: + + 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 = 'oai' + 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.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + AND ingest_request.base_url NOT LIKE '%edoc.mpg.de%' + AND ingest_request.base_url NOT LIKE '%doaj.org%' + AND ingest_request.base_url NOT LIKE '%orcid.org%' + AND ingest_request.base_url NOT LIKE '%gateway.isiknowledge.com%' + AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + success | 13258356 + no-pdf-link | 8685519 + no-capture | 4765663 + redirect-loop | 1557731 + terminal-bad-status | 803373 + link-loop | 453999 + wrong-mimetype | 440230 + null-body | 71457 + cdx-error | 18426 + | 15275 + petabox-error | 13408 + wayback-error | 11845 + blocked-cookie | 11580 + skip-url-blocklist | 7761 + wayback-content-error | 383 + spn2-cdx-lookup-failure | 362 + gateway-timeout | 320 + body-too-large | 207 + spn2-error:job-failed | 191 + redirects-exceeded | 120 + (20 rows) + +OAI-PMH compared to a couple weeks ago: + + 13258356-12872279 = +386,077 success + 8685519-9329602 = -644,083 no-pdf-link + 4765663-4696362 = +69,301 no-capture + 803373-660418 = +142,955 terminal-bad-status + +OA DOI 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 = 'doi' + AND ( + ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog' + ) + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------------+--------- + no-pdf-link | 6693547 + success | 5979016 + skip-url-blocklist | 3080986 + no-capture | 1876914 + redirect-loop | 1872817 + terminal-bad-status | 656674 + link-loop | 624290 + blocked-cookie | 448001 + gateway-timeout | 351896 + too-many-redirects | 307895 + forbidden | 306710 + spn2-cdx-lookup-failure | 301312 + cdx-error | 279766 + not-found | 273667 + wrong-mimetype | 83289 + spn2-error | 76806 + spn2-error:too-many-redirects | 58064 + wayback-error | 54278 + spn2-wayback-error | 51768 + remote-server-error | 45683 + (20 rows) + +OA DOI changes: + + 5979016-5690862 = +288,154 success + 6693547-10516478 = -3,822,931 no-pdf-link (still many!) + 1876914-1215179 = +661,735 no-capture + 3080986-265689 = +2,815,297 skip-url-blocklist + +Overall about half a million new 'success', pretty good. over 750k new +no-capture for crawling. + +## Seedlist Dumps + +Note that this is just seedlists, not full ingest requests. + + COPY ( + SELECT ingest_file_result.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_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' + ) + 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 '%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%' + + ) TO '/srv/sandcrawler/tasks/patch_2021-09-16_terminal_seedlist.txt'; + => 6,354,365 + +Then run the actual patch crawl! + +## Ingest Requests for Bulk Retry + +TODO: for each of the link sources mentioned at top, do a separate query by +source to re-ingest. |