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-rw-r--r--notes/ingest/2021-08_mag.md276
-rw-r--r--notes/ingest/2021-08_oai_pmh_patch.md204
2 files changed, 480 insertions, 0 deletions
diff --git a/notes/ingest/2021-08_mag.md b/notes/ingest/2021-08_mag.md
new file mode 100644
index 0000000..5bab4f0
--- /dev/null
+++ b/notes/ingest/2021-08_mag.md
@@ -0,0 +1,276 @@
+
+Using 2021-06-07 upstream MAG snapshot to run a crawl and do some re-ingest.
+Also want to re-ingest some old/failed ingests, now that pipeline/code has
+improved.
+
+Ran munging from `scratch:ingest/mag` notes first. Yielded 22.5M PDF URLs.
+
+
+## Persist Ingest Requests
+
+ zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | head -n1000 | pv -l | ./persist_tool.py ingest-request -
+ => Worker: Counter({'total': 1000, 'insert-requests': 276, 'update-requests': 0})
+ => JSON lines pushed: Counter({'total': 1000, 'pushed': 1000})
+
+ zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | pv -l | ./persist_tool.py ingest-request -
+ => 22.5M 0:46:00 [8.16k/s]
+ => Worker: Counter({'total': 22527585, 'insert-requests': 8686315, 'update-requests': 0})
+ => JSON lines pushed: Counter({'total': 22527585, 'pushed': 22527585})
+
+Roughly 8.6 million new URLs
+
+## Pre-Crawl Status Counts
+
+Status of combined old and new requests, with some large domains removed:
+
+ 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 = 'mag'
+ 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 '%researchgate.net%'
+ AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
+ AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
+ AND ingest_request.base_url NOT LIKE '%link.springer.com%'
+ AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
+ -- AND ingest_request.created > '2021-06-01'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------------+----------
+ success | 26123975
+ | 6664846
+ no-pdf-link | 1859908
+ redirect-loop | 1532405
+ no-capture | 1199126
+ link-loop | 1157010
+ terminal-bad-status | 832362
+ gateway-timeout | 202158
+ spn2-cdx-lookup-failure | 81406
+ wrong-mimetype | 69087
+ invalid-host-resolution | 37262
+ wayback-error | 21340
+ petabox-error | 11237
+ null-body | 9414
+ wayback-content-error | 2199
+ cdx-error | 1893
+ spn2-error | 1741
+ spn2-error:job-failed | 971
+ blocked-cookie | 902
+ spn2-error:invalid-url-syntax | 336
+ (20 rows)
+
+And just the new URLs (note that domain filter shouldn't be required, but
+keeping for consistency):
+
+ 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 = 'mag'
+ 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 '%researchgate.net%'
+ AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
+ AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
+ AND ingest_request.base_url NOT LIKE '%link.springer.com%'
+ AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
+ AND ingest_request.created > '2021-06-01'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------+---------
+ | 6664780
+ success | 1957844
+ redirect-loop | 23357
+ terminal-bad-status | 9385
+ no-pdf-link | 8315
+ no-capture | 6892
+ link-loop | 4517
+ wrong-mimetype | 3864
+ cdx-error | 1749
+ blocked-cookie | 842
+ null-body | 747
+ wayback-error | 688
+ wayback-content-error | 570
+ gateway-timeout | 367
+ petabox-error | 340
+ spn2-cdx-lookup-failure | 150
+ read-timeout | 122
+ not-found | 119
+ invalid-host-resolution | 63
+ spn2-error | 23
+ (20 rows)
+
+## Dump Initial Bulk Ingest Requests
+
+Note that this is all-time, not just recent, and will re-process a lot of
+"no-pdf-link":
+
+ 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 = 'mag'
+ AND (
+ ingest_file_result.status IS NULL
+ OR ingest_file_result.status = 'no-pdf-link'
+ OR ingest_file_result.status = 'cdx-error'
+ )
+ 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 '%researchgate.net%'
+ AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
+ AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
+ AND ingest_request.base_url NOT LIKE '%link.springer.com%'
+ AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
+ ) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json';
+ => COPY 8526647
+
+Transform to ingest requests:
+
+ ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.ingest_request.json
+ => 8.53M 0:03:40
+
+Enqueue the whole batch:
+
+ cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.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
+
+Updated stats after running initial 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 = 'mag'
+ 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 '%researchgate.net%'
+ AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
+ AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
+ AND ingest_request.base_url NOT LIKE '%link.springer.com%'
+ AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
+ AND ingest_request.created > '2021-06-01'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------+---------
+ success | 5184994
+ no-capture | 3284416
+ redirect-loop | 98685
+ terminal-bad-status | 28733
+ link-loop | 28518
+ blocked-cookie | 22338
+ no-pdf-link | 19073
+ wrong-mimetype | 9122
+ null-body | 2793
+ wayback-error | 2128
+ wayback-content-error | 1233
+ cdx-error | 1198
+ petabox-error | 617
+ gateway-timeout | 395
+ not-found | 130
+ read-timeout | 128
+ | 111
+ invalid-host-resolution | 63
+ spn2-cdx-lookup-failure | 24
+ spn2-error | 20
+ (20 rows)
+
+## Generate Seedlist
+
+For crawling, do a similar (but not identical) dump:
+
+ 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 = 'mag'
+ AND (
+ ingest_file_result.status IS NULL
+ OR 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'
+ )
+ 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 '%researchgate.net%'
+ AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%'
+ AND ingest_request.base_url NOT LIKE '%omicsonline.org%'
+ AND ingest_request.base_url NOT LIKE '%link.springer.com%'
+ AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%'
+ ) t1
+ ) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json';
+ => COPY 4599519
+
+Prep ingest requests (for post-crawl use):
+
+ ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | pv -l > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.ingest_request.json
+ => 4.60M 0:02:55 [26.2k/s]
+
+And actually dump seedlist(s):
+
+ cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt
+ cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt
+ cat /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt
+ => DONE
+
+ wc -l /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.*.txt
+ 4593238 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt
+ 4632911 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt
+ 3294710 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt
diff --git a/notes/ingest/2021-08_oai_pmh_patch.md b/notes/ingest/2021-08_oai_pmh_patch.md
new file mode 100644
index 0000000..20bb451
--- /dev/null
+++ b/notes/ingest/2021-08_oai_pmh_patch.md
@@ -0,0 +1,204 @@
+
+Just a "patch" of previous OAI-PMH crawl/ingest: re-ingesting and potentially
+re-crawling content which failed to ingest the first time.
+
+## Basic Counts
+
+ 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.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%'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------+----------
+ success | 14143967
+ no-pdf-link | 12857899
+ no-capture | 5501279
+ redirect-loop | 2092667
+ terminal-bad-status | 747387
+ wrong-mimetype | 597212
+ link-loop | 542143
+ null-body | 93566
+ cdx-error | 20514
+ petabox-error | 18387
+ | 15283
+ wayback-error | 13996
+ gateway-timeout | 510
+ skip-url-blocklist | 184
+ wayback-content-error | 145
+ bad-redirect | 137
+ redirects-exceeded | 120
+ bad-gzip-encoding | 116
+ timeout | 80
+ spn2-cdx-lookup-failure | 58
+ (20 rows)
+
+
+ SELECT
+ oai_prefix,
+ COUNT(CASE WHEN status = 'success' THEN 1 END) as success,
+ COUNT(*) as total
+ FROM (
+ SELECT
+ ingest_file_result.status as status,
+ -- eg "oai:cwi.nl:4881"
+ substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix
+ 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.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%'
+ ) t1
+ GROUP BY oai_prefix
+ ORDER BY total DESC
+ LIMIT 25;
+
+ oai_prefix | success | total
+ --------------------------+---------+---------
+ repec | 1133019 | 2783448
+ hal | 573019 | 1049607
+ hsp.org | 0 | 810281
+ www.irgrid.ac.cn | 18007 | 748828
+ cds.cern.ch | 74078 | 688091
+ americanae.aecid.es | 71309 | 572792
+ juser.fz-juelich.de | 23026 | 518551
+ espace.library.uq.edu.au | 6645 | 508960
+ igi.indrastra.com | 59626 | 478577
+ archive.ugent.be | 65269 | 424014
+ hrcak.srce.hr | 403719 | 414897
+ zir.nsk.hr | 156753 | 397200
+ renati.sunedu.gob.pe | 79362 | 388355
+ hypotheses.org | 3 | 374296
+ rour.neicon.ru | 7997 | 354529
+ generic.eprints.org | 263564 | 340470
+ invenio.nusl.cz | 6340 | 325867
+ evastar-karlsruhe.de | 62277 | 317952
+ quod.lib.umich.edu | 5 | 309135
+ diva.org | 67917 | 298348
+ t2r2.star.titech.ac.jp | 1085 | 289388
+ edpsciences.org | 139495 | 284972
+ repository.ust.hk | 10243 | 283417
+ revues.org | 151156 | 277497
+ pure.atira.dk | 13492 | 260754
+ (25 rows)
+
+Top counts by OAI prefix and status:
+
+ SELECT
+ oai_prefix,
+ status,
+ COUNT((oai_prefix,status))
+ FROM (
+ SELECT
+ ingest_file_result.status as status,
+ -- eg "oai:cwi.nl:4881"
+ substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix
+ 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.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%'
+ ) t1
+ GROUP BY oai_prefix, status
+ ORDER BY COUNT DESC
+ LIMIT 40;
+
+
+ oai_prefix | status | count
+ ---------------------------+---------------+---------
+ repec | success | 1133019
+ hsp.org | no-pdf-link | 794781
+ repec | no-pdf-link | 638124
+ hal | success | 573020
+ cds.cern.ch | no-capture | 540380
+ repec | redirect-loop | 516434
+ juser.fz-juelich.de | no-pdf-link | 477881
+ americanae.aecid.es | no-pdf-link | 417766
+ hrcak.srce.hr | success | 403720
+ www.irgrid.ac.cn | no-pdf-link | 370908
+ hal | no-pdf-link | 359261
+ www.irgrid.ac.cn | no-capture | 355532
+ espace.library.uq.edu.au | no-pdf-link | 320479
+ igi.indrastra.com | no-pdf-link | 318242
+ repec | no-capture | 317062
+ invenio.nusl.cz | no-pdf-link | 309802
+ rour.neicon.ru | redirect-loop | 300911
+ hypotheses.org | no-pdf-link | 300251
+ renati.sunedu.gob.pe | no-capture | 282800
+ t2r2.star.titech.ac.jp | no-pdf-link | 272045
+ generic.eprints.org | success | 263564
+ quod.lib.umich.edu | no-pdf-link | 259661
+ archive.ugent.be | no-capture | 256164
+ evastar-karlsruhe.de | no-pdf-link | 248939
+ zir.nsk.hr | link-loop | 226919
+ repository.ust.hk | no-pdf-link | 208569
+ edoc.mpg.de | no-pdf-link | 199758
+ bibliotecadigital.jcyl.es | no-pdf-link | 188433
+ orbi.ulg.ac.be | no-pdf-link | 172373
+ diva.org | no-capture | 171115
+ lup.lub.lu.se | no-pdf-link | 168652
+ erudit.org | success | 168490
+ ojs.pkp.sfu.ca | success | 168029
+ lib.dr.iastate.edu | success | 158494
+ zir.nsk.hr | success | 156753
+ digital.kenyon.edu | success | 154900
+ revues.org | success | 151156
+ books.openedition.org | no-pdf-link | 149607
+ freidok.uni-freiburg.de | no-pdf-link | 146837
+ digitalcommons.unl.edu | success | 144025
+ (40 rows)
+
+TODO: also exclude:
+
+ oai:nsp.org: (philly historical society)
+
+TODO: more rows for success/total query (aka, increase LIMIT)
+
+TODO: wait until MAG crawl is complete to re-run ingest? otherwise many
+no-capture may actually be (recently) captured. depends on size of MAG crawl I
+guess.
+
+TODO: just delete the "excluded" rows?
+TODO: do some spot-sampling of 'no-pdf-link' domains, see if newer sandcrawler works
+TODO: do random sampling of 'no-pdf-link' URLs, see if newer sandcrawler works
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-22 04:02:10 +0000