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+
+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.