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-rw-r--r--notes/ingest/2020-02-04_ingest_backfills.md (renamed from notes/tasks/2020-02-04_ingest_backfills.md)0
-rw-r--r--notes/ingest/2020-02-14_unpaywall_ingest.md60
-rw-r--r--notes/ingest/2020-02-18_ingest_backfills.md (renamed from notes/tasks/2020-02-18_ingest_backfills.md)0
-rw-r--r--notes/ingest/2020-02-21_ingest_backfills.md (renamed from notes/tasks/2020-02-21_ingest_backfills.md)0
-rw-r--r--notes/ingest/2020-02-22_fixed_domain.txt246
-rw-r--r--notes/ingest/2020-03-02_ingests.txt174
6 files changed, 480 insertions, 0 deletions
diff --git a/notes/tasks/2020-02-04_ingest_backfills.md b/notes/ingest/2020-02-04_ingest_backfills.md
index 73a42ef..73a42ef 100644
--- a/notes/tasks/2020-02-04_ingest_backfills.md
+++ b/notes/ingest/2020-02-04_ingest_backfills.md
diff --git a/notes/ingest/2020-02-14_unpaywall_ingest.md b/notes/ingest/2020-02-14_unpaywall_ingest.md
new file mode 100644
index 0000000..df4795b
--- /dev/null
+++ b/notes/ingest/2020-02-14_unpaywall_ingest.md
@@ -0,0 +1,60 @@
+
+## Stats and Things
+
+ zcat unpaywall_snapshot_2019-11-22T074546.jsonl.gz | jq .oa_locations[].url_for_pdf -r | rg -v ^null | cut -f3 -d/ | sort | uniq -c | sort -nr > top_domains.txt
+
+## Transform
+
+ zcat unpaywall_snapshot_2019-11-22T074546.jsonl.gz | ./unpaywall2ingestrequest.py - | pv -l > /dev/null
+ => 22M 1:31:25 [ 4k/s]
+
+Shard it into batches of roughly 1 million (all are 1098096 +/- 1):
+
+ zcat unpaywall_snapshot_2019-11-22.ingest_request.shuf.json.gz | split -n r/20 -d - unpaywall_snapshot_2019-11-22.ingest_request.split_ --additional-suffix=.json
+
+Test ingest:
+
+ head -n200 unpaywall_snapshot_2019-11-22.ingest_request.split_00.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+Add a single batch like:
+
+ cat unpaywall_snapshot_2019-11-22.ingest_request.split_00.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+## Progress/Status
+
+There are 21,961,928 lines total, in batches of 1,098,097.
+
+ unpaywall_snapshot_2019-11-22.ingest_request.split_00.json
+ => 2020-02-24 21:05 local: 1,097,523 ~22 results/sec (combined)
+ => 2020-02-25 10:35 local: 0
+ unpaywall_snapshot_2019-11-22.ingest_request.split_01.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_02.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_03.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_04.json
+ => 2020-02-25 11:26 local: 4,388,997
+ => 2020-02-25 10:14 local: 1,115,821
+ => 2020-02-26 16:00 local: 265,116
+ unpaywall_snapshot_2019-11-22.ingest_request.split_05.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_06.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_07.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_08.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_09.json
+ => 2020-02-26 16:01 local: 6,843,708
+ => 2020-02-26 16:31 local: 4,839,618
+ => 2020-02-28 10:30 local: 2,619,319
+ unpaywall_snapshot_2019-11-22.ingest_request.split_10.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_11.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_12.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_13.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_14.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_15.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_16.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_17.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_18.json
+ unpaywall_snapshot_2019-11-22.ingest_request.split_19.json
+ => 2020-02-28 10:50 local: 13,551,887
+ => 2020-03-01 23:38 local: 4,521,076
+ => 2020-03-02 10:45 local: 2,827,071
+ => 2020-03-02 21:06 local: 1,257,176
+ added about 500k bulk re-ingest to try and work around cdx errors
+ => 2020-03-02 21:30 local: 1,733,654
diff --git a/notes/tasks/2020-02-18_ingest_backfills.md b/notes/ingest/2020-02-18_ingest_backfills.md
index 1ab18f4..1ab18f4 100644
--- a/notes/tasks/2020-02-18_ingest_backfills.md
+++ b/notes/ingest/2020-02-18_ingest_backfills.md
diff --git a/notes/tasks/2020-02-21_ingest_backfills.md b/notes/ingest/2020-02-21_ingest_backfills.md
index 48df910..48df910 100644
--- a/notes/tasks/2020-02-21_ingest_backfills.md
+++ b/notes/ingest/2020-02-21_ingest_backfills.md
diff --git a/notes/ingest/2020-02-22_fixed_domain.txt b/notes/ingest/2020-02-22_fixed_domain.txt
new file mode 100644
index 0000000..a60de42
--- /dev/null
+++ b/notes/ingest/2020-02-22_fixed_domain.txt
@@ -0,0 +1,246 @@
+
+www.degruyter.com
+
+ "/view/books/" didn't have citation_pdf_url, so added custom URL rule.
+
+ Not sure why redirect-loop happening, but isn't with current live ingest
+ tool?
+
+ domain | status | count
+ -------------------+-------------------------+-------
+ www.degruyter.com | redirect-loop | 22023
+ www.degruyter.com | no-pdf-link | 8773
+ www.degruyter.com | no-capture | 8617
+ www.degruyter.com | success | 840
+ www.degruyter.com | link-loop | 59
+ www.degruyter.com | terminal-bad-status | 23
+ www.degruyter.com | wrong-mimetype | 12
+ www.degruyter.com | spn-error | 4
+ www.degruyter.com | spn2-cdx-lookup-failure | 4
+ www.degruyter.com | spn2-error:proxy-error | 1
+ www.degruyter.com | spn-remote-error | 1
+ www.degruyter.com | gateway-timeout | 1
+ www.degruyter.com | petabox-error | 1
+ (13 rows)
+
+www.frontiersin.org
+
+ no pdf link
+
+ seems to live ingest fine? files served from "*.blob.core.windows.net"
+ no fix, just re-ingest.
+
+ domain | status | count
+ ---------------------+-------------------------+-------
+ www.frontiersin.org | no-pdf-link | 17503
+ www.frontiersin.org | terminal-bad-status | 6696
+ www.frontiersin.org | wayback-error | 203
+ www.frontiersin.org | no-capture | 20
+ www.frontiersin.org | spn-error | 6
+ www.frontiersin.org | gateway-timeout | 3
+ www.frontiersin.org | wrong-mimetype | 3
+ www.frontiersin.org | spn2-cdx-lookup-failure | 2
+ www.frontiersin.org | spn2-error:job-failed | 2
+ www.frontiersin.org | spn-remote-error | 1
+ www.frontiersin.org | cdx-error | 1
+ (11 rows)
+
+www.mdpi.com
+
+ terminal-bad-status
+
+ Seems to ingest fine live? No fix, just re-ingest.
+
+ domain | status | count
+ --------------+-------------------------+-------
+ www.mdpi.com | terminal-bad-status | 13866
+ www.mdpi.com | wrong-mimetype | 2693
+ www.mdpi.com | wayback-error | 513
+ www.mdpi.com | redirect-loop | 505
+ www.mdpi.com | success | 436
+ www.mdpi.com | no-capture | 214
+ www.mdpi.com | no-pdf-link | 43
+ www.mdpi.com | spn2-cdx-lookup-failure | 34
+ www.mdpi.com | gateway-timeout | 3
+ www.mdpi.com | petabox-error | 2
+ (10 rows)
+
+www.ahajournals.org | no-pdf-link | 5727
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1
+ WHERE t1.domain = 'www.ahajournals.org'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC;
+
+ SELECT * FROM ingest_file_result
+ WHERE terminal_url LIKE '%www.ahajournals.org%'
+ AND status = 'no-pdf-link'
+ ORDER BY updated DESC
+ LIMIT 10;
+
+ domain | status | count
+ ---------------------+----------------+-------
+ www.ahajournals.org | no-pdf-link | 5738
+ www.ahajournals.org | wrong-mimetype | 84
+ (2 rows)
+
+
+ pdf | https://doi.org/10.1161/circ.110.19.2977 | 2020-02-23 00:28:55.256296+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 |
+ pdf | https://doi.org/10.1161/str.49.suppl_1.tp403 | 2020-02-23 00:27:34.950059+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 |
+ pdf | https://doi.org/10.1161/str.49.suppl_1.tp168 | 2020-02-23 00:25:54.611271+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 |
+ pdf | https://doi.org/10.1161/jaha.119.012131 | 2020-02-23 00:24:44.244511+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 |
+
+ Ah, the ol' annoying 'cookieAbsent'. Works with live SPNv2 via soft-404
+ detection, but that status wasn't coming through, and needed custom
+ pdf-link detection.
+
+ FIXED: added pdf-link detection
+
+ehp.niehs.nih.gov | no-pdf-link | 5772
+
+ simple custom URL format. but are they also blocking?
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1
+ WHERE t1.domain = 'ehp.niehs.nih.gov'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC;
+
+ domain | status | count
+ -------------------+----------------+-------
+ ehp.niehs.nih.gov | no-pdf-link | 5791
+ ehp.niehs.nih.gov | wrong-mimetype | 11
+ (2 rows)
+
+ FIXED: mostly just slow, custom URL seems to work
+
+journals.tsu.ru | no-pdf-link | 4404
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1
+ WHERE t1.domain = 'journals.tsu.ru'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC;
+
+ SELECT * FROM ingest_file_result
+ WHERE terminal_url LIKE '%journals.tsu.ru%'
+ AND status = 'no-pdf-link'
+ ORDER BY updated DESC
+ LIMIT 10;
+
+ domain | status | count
+ -----------------+----------------+-------
+ journals.tsu.ru | no-pdf-link | 4409
+ journals.tsu.ru | success | 1
+ journals.tsu.ru | wrong-mimetype | 1
+ (3 rows)
+
+
+ pdf | https://doi.org/10.17223/18572685/57/3 | 2020-02-23 00:45:49.003593+00 | f | no-pdf-link | http://journals.tsu.ru/rusin/&journal_page=archive&id=1907&article_id=42847 | 20200213132322 | 200 |
+ pdf | https://doi.org/10.17223/17267080/71/4 | 2020-02-23 00:31:25.715416+00 | f | no-pdf-link | http://journals.tsu.ru/psychology/&journal_page=archive&id=1815&article_id=40405 | 20200211151825 | 200 |
+ pdf | https://doi.org/10.17223/15617793/399/33 | 2020-02-23 00:29:45.414865+00 | f | no-pdf-link | http://journals.tsu.ru/vestnik/&journal_page=archive&id=1322&article_id=24619 | 20200208152715 | 200 |
+ pdf | https://doi.org/10.17223/19988613/58/15 | 2020-02-23 00:25:24.402838+00 | f | no-pdf-link | http://journals.tsu.ru//history/&journal_page=archive&id=1827&article_id=40501 | 20200212200320 | 200 |
+
+ FIXED: simple new custom PDF link pattern
+
+www.cogentoa.com | no-pdf-link | 4282
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1
+ WHERE t1.domain = 'www.cogentoa.com'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC;
+
+ SELECT * FROM ingest_file_result
+ WHERE terminal_url LIKE '%www.cogentoa.com%'
+ AND status = 'no-pdf-link'
+ ORDER BY updated DESC
+ LIMIT 10;
+
+ domain | status | count
+ ------------------+-------------+-------
+ www.cogentoa.com | no-pdf-link | 4296
+ (1 row)
+
+ pdf | https://doi.org/10.1080/23311932.2015.1022632 | 2020-02-23 01:06:14.040013+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311932.2015.1022632 | 20200208054228 | 200 |
+ pdf | https://doi.org/10.1080/23322039.2020.1730079 | 2020-02-23 01:04:53.754117+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23322039.2020.1730079 | 20200223010431 | 200 |
+ pdf | https://doi.org/10.1080/2331186x.2018.1460901 | 2020-02-23 01:04:03.47563+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/2331186X.2018.1460901 | 20200207200958 | 200 |
+ pdf | https://doi.org/10.1080/23311975.2017.1412873 | 2020-02-23 01:03:08.063545+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311975.2017.1412873 | 20200209034602 | 200 |
+ pdf | https://doi.org/10.1080/23311916.2017.1293481 | 2020-02-23 01:02:42.868424+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311916.2017.1293481 | 20200208101623 | 200 |
+
+ FIXED: simple custom URL-based pattern
+
+chemrxiv.org | no-pdf-link | 4186
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1
+ WHERE t1.domain = 'chemrxiv.org'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC;
+
+ SELECT * FROM ingest_file_result
+ WHERE terminal_url LIKE '%chemrxiv.org%'
+ AND status = 'no-pdf-link'
+ ORDER BY updated DESC
+ LIMIT 10;
+
+ domain | status | count
+ --------------+-------------------------+-------
+ chemrxiv.org | no-pdf-link | 4202
+ chemrxiv.org | wrong-mimetype | 64
+ chemrxiv.org | wayback-error | 14
+ chemrxiv.org | success | 12
+ chemrxiv.org | terminal-bad-status | 4
+ chemrxiv.org | spn2-cdx-lookup-failure | 1
+
+ pdf | https://doi.org/10.26434/chemrxiv.9912812.v1 | 2020-02-23 01:08:34.585084+00 | f | no-pdf-link | https://chemrxiv.org/articles/Proximity_Effect_in_Crystalline_Framework_Materials_Stacking-Induced_Functionality_in_MOFs_and_COFs/9912812/1 | 20200215072929 | 200 |
+ pdf | https://doi.org/10.26434/chemrxiv.7150097 | 2020-02-23 01:05:48.957624+00 | f | no-pdf-link | https://chemrxiv.org/articles/Systematic_Engineering_of_a_Protein_Nanocage_for_High-Yield_Site-Specific_Modification/7150097 | 20200213002430 | 200 |
+ pdf | https://doi.org/10.26434/chemrxiv.7833500.v1 | 2020-02-23 00:55:41.013109+00 | f | no-pdf-link | https://chemrxiv.org/articles/Formation_of_Neutral_Peptide_Aggregates_Studied_by_Mass_Selective_IR_Action_Spectroscopy/7833500/1 | 20200210131343 | 200 |
+ pdf | https://doi.org/10.26434/chemrxiv.8146103 | 2020-02-23 00:52:00.193328+00 | f | no-pdf-link | https://chemrxiv.org/articles/On-Demand_Guest_Release_from_MOF-5_Sealed_with_Nitrophenylacetic_Acid_Photocapping_Groups/8146103 | 20200207215449 | 200 |
+ pdf | https://doi.org/10.26434/chemrxiv.10101419 | 2020-02-23 00:46:14.086913+00 | f | no-pdf-link | https://chemrxiv.org/articles/Biradical_Formation_by_Deprotonation_in_Thiazole-Derivatives_The_Hidden_Nature_of_Dasatinib/10101419 | 20200214044153 | 200 |
+
+ FIXED: complex JSON PDF url extraction; maybe for all figshare?
+
+TODO:
+x many datacite prefixes go to IRs, but have is_oa:false. we should probably crawl by default based on release_type
+ => fatcat branch bnewbold-more-ingest
+- re-ingest all degruyter (doi_prefix:10.1515)
+ 1456169 doi:10.1515\/*
+ 89942 doi:10.1515\/* is_oa:true
+ 36350 doi:10.1515\/* in_ia:false is_oa:true
+ 1290830 publisher:Gruyter
+ 88944 publisher:Gruyter is_oa:true
+ 40034 publisher:Gruyter is_oa:true in_ia:false
+- re-ingest all frontiersin
+ 248165 publisher:frontiers
+ 161996 publisher:frontiers is_oa:true
+ 36093 publisher:frontiers is_oa:true in_ia:false
+ 121001 publisher:frontiers in_ia:false
+- re-ingest all mdpi
+ 43114 publisher:mdpi is_oa:true in_ia:false
+- re-ingest all ahajournals.org
+ 132000 doi:10.1161\/*
+ 6606 doi:10.1161\/* in_ia:false is_oa:true
+ 81349 publisher:"American Heart Association"
+ 5986 publisher:"American Heart Association" is_oa:true in_ia:false
+- re-ingest all ehp.niehs.nih.gov
+ 25522 doi:10.1289\/*
+ 15315 publisher:"Environmental Health Perspectives"
+ 8779 publisher:"Environmental Health Perspectives" in_ia:false
+ 12707 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true
+- re-ingest all journals.tsu.ru
+ 12232 publisher:"Tomsk State University"
+ 11668 doi:10.17223\/*
+ 4861 publisher:"Tomsk State University" in_ia:false is_oa:true
+- re-ingest all www.cogentoa.com
+ 3421898 doi:10.1080\/*
+ 4602 journal:cogent is_oa:true in_ia:false
+ 5631 journal:cogent is_oa:true (let's recrawl all from publisher domain)
+- re-ingest chemrxiv
+ 8281 doi:10.26434\/chemrxiv*
+ 6918 doi:10.26434\/chemrxiv* in_ia:false
+
+Submit all the above with limits of 1000, then follow up later to check that
+there was success?
+
diff --git a/notes/ingest/2020-03-02_ingests.txt b/notes/ingest/2020-03-02_ingests.txt
new file mode 100644
index 0000000..e98ef33
--- /dev/null
+++ b/notes/ingest/2020-03-02_ingests.txt
@@ -0,0 +1,174 @@
+
+## protocols.io
+
+Tested that single ingest is working, and they fixed PDF format on their end
+recently.
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --name protocols.io
+ => Expecting 8448 release objects in search queries
+ => Counter({'estimate': 8448, 'kafka': 8448, 'ingest_request': 8448, 'elasticsearch_release': 8448})
+
+## backfill follow-ups
+
+- re-ingest all degruyter (doi_prefix:10.1515)
+ 89942 doi:10.1515\/* is_oa:true
+ 36350 doi:10.1515\/* in_ia:false is_oa:true
+ 40034 publisher:Gruyter is_oa:true in_ia:false
+ => update:
+ 135926 doi:10.1515\/* is_oa:true
+ 50544 doi:10.1515\/* in_ia:false is_oa:true
+ 54880 publisher:Gruyter is_oa:true in_ia:false
+- re-ingest all frontiersin
+ 36093 publisher:frontiers is_oa:true in_ia:false
+ => update
+ 22444 publisher:frontiers is_oa:true in_ia:false
+ 22029 doi_prefix:10.3389 is_oa:true in_ia:false
+
+ select status, count(*) from ingest_file_result where base_url like 'https://doi.org/10.3389/%' group by status order by count(*) desc;
+
+ status | count
+ -------------------------------------+-------
+ success | 34721
+ no-pdf-link | 18157
+ terminal-bad-status | 6799
+ cdx-error | 1805
+ wayback-error | 333
+ no-capture | 301
+ [...]
+
+ select * from ingest_file_result where base_url like 'https://doi.org/10.17723/aarc%' and status = 'no-pdf-link' order by updated desc limit 100;
+
+- re-ingest all mdpi
+ 43114 publisher:mdpi is_oa:true in_ia:false
+ => update
+ 8548 publisher:mdpi is_oa:true in_ia:false
+
+ select status, count(*) from ingest_file_result where base_url like 'https://doi.org/10.3390/%' group by status order by count(*) desc;
+ status | count
+ -------------------------------------+--------
+ success | 108971
+ cdx-error | 6655
+ wrong-mimetype | 3359
+ terminal-bad-status | 1299
+ wayback-error | 151
+ spn2-cdx-lookup-failure | 87
+
+ => added hack for gzip content-encoding coming through pdf fetch
+ => will re-ingest all after pushing fix
+
+- re-ingest all ahajournals.org
+ 132000 doi:10.1161\/*
+ 6606 doi:10.1161\/* in_ia:false is_oa:true
+ 81349 publisher:"American Heart Association"
+ 5986 publisher:"American Heart Association" is_oa:true in_ia:false
+ => update
+ 1337 publisher:"American Heart Association" is_oa:true in_ia:false
+
+ status | count
+ -------------------------------------+-------
+ success | 1480
+ cdx-error | 1176
+ spn2-cdx-lookup-failure | 514
+ no-pdf-link | 85
+ wayback-error | 25
+ spn2-error:job-failed | 18
+
+ => will re-run errors
+- re-ingest all ehp.niehs.nih.gov
+ 25522 doi:10.1289\/*
+ 15315 publisher:"Environmental Health Perspectives"
+ 8779 publisher:"Environmental Health Perspectives" in_ia:false
+ 12707 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true
+ => update
+ 7547 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true
+- re-ingest all journals.tsu.ru
+ 12232 publisher:"Tomsk State University"
+ 11668 doi:10.17223\/*
+ 4861 publisher:"Tomsk State University" in_ia:false is_oa:true
+ => update
+ 2605 publisher:"Tomsk State University" in_ia:false is_oa:true
+ => just need to retry these? seem fine
+- re-ingest all www.cogentoa.com
+ 3421898 doi:10.1080\/*
+ 4602 journal:cogent is_oa:true in_ia:false
+ 5631 journal:cogent is_oa:true (let's recrawl all from publisher domain)
+ => update
+ 254 journal:cogent is_oa:true in_ia:false
+- re-ingest chemrxiv
+ 8281 doi:10.26434\/chemrxiv*
+ 6918 doi:10.26434\/chemrxiv* in_ia:false
+ => update
+ 4890 doi:10.26434\/chemrxiv* in_ia:false
+ => re-ingest
+ => allow non-OA
+
+ # american archivist
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4
+ Counter({'estimate': 2920, 'elasticsearch_release': 2920, 'kafka': 2911, 'ingest_request': 2911})
+ => 2020-02-04: 85 / 3,005
+ => 2020-03-02: 2,182 / 3,005 preserved. some no-pdf-link, otherwise just a bunch of spn2-error
+ => looks like the no-pdf-url due to pinnacle-secure.allenpress.com soft-blocking loop
+
+
+## backfill re-ingests
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa --force-recrawl container --container-id zpobyv4vbranllc7oob56tgci4
+ => Counter({'elasticsearch_release': 823, 'estimate': 823, 'ingest_request': 814, 'kafka': 814})
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter
+ => Counter({'elasticsearch_release': 54880, 'estimate': 54880, 'kafka': 51497, 'ingest_request': 51497})
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query 'publisher:"Tomsk State University"'
+ => Counter({'ingest_request': 2605, 'kafka': 2605, 'elasticsearch_release': 2605, 'estimate': 2605})
+
+ ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*"
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi
+ => Counter({'estimate': 8548, 'elasticsearch_release': 8548, 'ingest_request': 6693, 'kafka': 6693})
+ => NOTE: about 2k not enqueued
+
+## re-ingest all broken
+
+ COPY (
+ SELECT row_to_json(ingest_request.*) FROM ingest_request
+ LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+ WHERE ingest_request.ingest_type = 'pdf'
+ AND ingest_file_result.ingest_type = 'pdf'
+ AND ingest_file_result.updated < NOW() - '1 day'::INTERVAL
+ AND ingest_file_result.hit = false
+ AND ingest_file_result.status like 'spn2-%'
+ ) TO '/grande/snapshots/reingest_spn2_20200302.rows.json';
+ => COPY 14849
+
+ COPY (
+ SELECT row_to_json(ingest_request.*) FROM ingest_request
+ LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+ WHERE ingest_request.ingest_type = 'pdf'
+ AND ingest_file_result.ingest_type = 'pdf'
+ AND ingest_file_result.hit = false
+ AND ingest_file_result.status like 'cdx-error'
+ ) TO '/grande/snapshots/reingest_cdxerr_20200302.rows.json';
+ => COPY 507610
+
+ This is a huge number! Re-ingest via bulk?
+
+Transform:
+
+ ./scripts/ingestrequest_row2json.py /grande/snapshots/reingest_spn2_20200302.rows.json > reingest_spn2_20200302.json
+ ./scripts/ingestrequest_row2json.py /grande/snapshots/reingest_cdxerr_20200302.rows.json > reingest_cdxerr_20200302.json
+
+Push to kafka:
+
+ cat reingest_spn2err_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1
+ # accidentially also piped the above through ingest-file-requests-bulk...
+ # which could actually be bad
+ cat reingest_cdxerr_20200302.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+## biorxiv/medrxiv
+
+ 8026 doi:10.1101\/20*
+ 2159 doi:10.1101\/20* in_ia:false
+
+ ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 'doi:10.1101\/20* in_ia:false'
+ => Counter({'estimate': 2159, 'ingest_request': 2159, 'elasticsearch_release': 2159, 'kafka': 2159})
+
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-22 19:38:07 +0000