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-rw-r--r--notes/ingest/2019-10-23_testing.md (renamed from notes/ingest/20191023_testing.md)0
-rw-r--r--notes/ingest/2020-01-14_bulk.md (renamed from notes/ingest/20200114_bulk_ingests.md)0
-rw-r--r--notes/ingest/2020-02_unpaywall.md (renamed from notes/ingest/2020-02-14_unpaywall_ingest.md)0
-rw-r--r--notes/ingest/2020-03-oa_but_not_marked.md25
-rw-r--r--notes/ingest/2020-03_mag.md (renamed from notes/ingest/2020-03-04_mag.md)168
-rw-r--r--notes/ingest/2020-03_s2.md (renamed from notes/ingest/2020-03_s2_ingest.md)0
-rw-r--r--notes/ingest/2020-04-07_datacite.md18
-rw-r--r--notes/ingest/2020-04-07_unpaywall.md63
-rw-r--r--notes/ingest/2020-04_datacite.md121
-rw-r--r--notes/ingest/2020-04_unpaywall.md129
-rw-r--r--notes/ingest/2020-05_oai_pmh.md125
-rw-r--r--notes/ingest/NEXT.md52
12 files changed, 620 insertions, 81 deletions
diff --git a/notes/ingest/20191023_testing.md b/notes/ingest/2019-10-23_testing.md
index 481c4e2..481c4e2 100644
--- a/notes/ingest/20191023_testing.md
+++ b/notes/ingest/2019-10-23_testing.md
diff --git a/notes/ingest/20200114_bulk_ingests.md b/notes/ingest/2020-01-14_bulk.md
index 9d05cda..9d05cda 100644
--- a/notes/ingest/20200114_bulk_ingests.md
+++ b/notes/ingest/2020-01-14_bulk.md
diff --git a/notes/ingest/2020-02-14_unpaywall_ingest.md b/notes/ingest/2020-02_unpaywall.md
index e18a2ff..e18a2ff 100644
--- a/notes/ingest/2020-02-14_unpaywall_ingest.md
+++ b/notes/ingest/2020-02_unpaywall.md
diff --git a/notes/ingest/2020-03-oa_but_not_marked.md b/notes/ingest/2020-03-oa_but_not_marked.md
new file mode 100644
index 0000000..73396bd
--- /dev/null
+++ b/notes/ingest/2020-03-oa_but_not_marked.md
@@ -0,0 +1,25 @@
+
+These are large journals with a high fraction of "in IA", but not marked as OA
+so not crawling regularly.
+
+TODO: add things like list of unpaywall ISSN / OA status to try and find more
+"practical" / bronze OA
+
+## First Run
+
+https://fatcat.wiki/container/vmv647omwrhzzgeclyrnpc4him
+https://fatcat.wiki/container/waxwzq3cnbet3cmwccpuk4bel4
+https://fatcat.wiki/container/hjoli2j6qffdpaalkszryuidk4
+https://fatcat.wiki/container/fci57bxfsffvzllbssocnfsr3e
+https://fatcat.wiki/container/hd23c57sunhcnar5fbgxsn36lm
+https://fatcat.wiki/container/bliguyxhonfb7ghuykxgtg3oqe
+
+## TODO
+
+https://fatcat.wiki/container/kn6dhptylrb77b5atyiom5ysjm no-pdf-link (but accessible)
+https://fatcat.wiki/container/s7bticdwizdmhll4taefg57jde no-pdf-link (easy?)
+
+https://fatcat.wiki/container/zm56axre7rgihh5sznxp65np5i large; no-pdf-link?
+https://fatcat.wiki/container/eb2lcnpf2zeezkmfckcvxw2pgi huge (20k+), not all OA?
+https://fatcat.wiki/container/adgy773dtra3xmrsynghcednqm broken?
+https://fatcat.wiki/container/w3gj5mynrnbtndalcc5jnhymym not OA? link-loop
diff --git a/notes/ingest/2020-03-04_mag.md b/notes/ingest/2020-03_mag.md
index 97594c8..428ce05 100644
--- a/notes/ingest/2020-03-04_mag.md
+++ b/notes/ingest/2020-03_mag.md
@@ -406,3 +406,171 @@ Full run:
2020-04-07 12:19 (pacific): 11,703,871
+## Post-bulk-ingest
+
+Around 2020-04-28, seems like main wave of bulk ingest is complete. Will need
+to re-try things like cdx-error.
+
+Current status:
+
+ status | count
+ -------------------------------+----------
+ success | 18491799
+ redirect-loop | 1968530
+ no-capture | 1373657
+ no-pdf-link | 1311842
+ link-loop | 1296439
+ terminal-bad-status | 627577
+ cdx-error | 418278
+ wrong-mimetype | 50141
+ wayback-error | 37159
+ petabox-error | 11249
+ null-body | 6295
+ gateway-timeout | 3051
+ spn2-cdx-lookup-failure | 328
+ spn2-error:invalid-url-syntax | 93
+ bad-redirect | 75
+ | 47
+ invalid-host-resolution | 28
+ spn2-error | 10
+ bad-gzip-encoding | 7
+ redirects-exceeded | 2
+ (20 rows)
+
+Lots of cdx-error to retry.
+
+The no-capture links are probably a mix of domain-blocklist and things that
+failed in bulk mode. Will dump and re-attempt them:
+
+
+ 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 = 'no-capture'
+ 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%'
+ ) TO '/grande/snapshots/mag_nocapture_20200420.rows.json';
+ => 859849
+
+What domains are these?
+
+ cat mag_nocapture_20200420.rows.json | jq .base_url -r | cut -f3 -d/ | sort | uniq -c | sort -nr | head -n30
+
+Let's filter down more:
+
+ cat mag_nocapture_20200420.rows.json | rg -v 'www.researchgate.net' | rg -v 'muse.jhu.edu' | rg -v 'www.omicsonline.org' | rg -v 'link.springer.com' | rg -v 'iopscience.iop.org' | rg -v 'ieeexplore.ieee.org' | shuf > mag_nocapture_20200420.rows.filtered.json
+
+ wc -l mag_nocapture_20200420.rows.filtered.json
+ 423085 mag_nocapture_20200420.rows.filtered.json
+
+Ok, enqueue!
+
+ cat mag_nocapture_20200420.rows.filtered.json | shuf | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1
+
+## Final Stats
+
+... for this round of 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'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+
+ status | count
+ -------------------------------------+----------
+ success | 18712849
+ redirect-loop | 2008110
+ no-pdf-link | 1337012
+ link-loop | 1326761
+ no-capture | 1030693
+ terminal-bad-status | 637143
+ gateway-timeout | 193194
+ cdx-error | 125907
+ spn2-cdx-lookup-failure | 77842
+ wrong-mimetype | 50882
+ wayback-error | 40278
+ invalid-host-resolution | 35201
+ petabox-error | 11254
+ null-body | 6485
+ spn2-error | 1643
+ spn2-error:job-failed | 747
+ spn2-error:invalid-url-syntax | 325
+ spn2-error:soft-time-limit-exceeded | 190
+ bad-redirect | 77
+ | 47
+ (20 rows)
+
+Failures by domain:
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (
+ SELECT
+ ingest_file_result.ingest_type,
+ ingest_file_result.status,
+ substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain
+ FROM ingest_file_result
+ LEFT JOIN ingest_request
+ ON ingest_file_result.ingest_type = ingest_request.ingest_type
+ AND ingest_file_result.base_url = ingest_request.base_url
+ WHERE
+ ingest_file_result.ingest_type = 'pdf'
+ AND ingest_request.link_source = 'mag'
+ ) t1
+ WHERE t1.domain != ''
+ AND t1.status != 'success'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC
+ LIMIT 30;
+
+
+ domain | status | count
+ ---------------------------------+---------------------+--------
+ ieeexplore.ieee.org | redirect-loop | 677712
+ cyberleninka.ru | link-loop | 308390
+ papers.ssrn.com | link-loop | 281804
+ ieeexplore.ieee.org | link-loop | 273559
+ dialnet.unirioja.es | redirect-loop | 240504
+ dialnet.unirioja.es | terminal-bad-status | 232481
+ onlinelibrary.wiley.com | no-pdf-link | 220932
+ iopscience.iop.org | terminal-bad-status | 172480
+ validate.perfdrive.com | no-pdf-link | 172312
+ link.springer.com | redirect-loop | 130398
+ agupubs.onlinelibrary.wiley.com | no-pdf-link | 113382
+ iopscience.iop.org | redirect-loop | 105234
+ www.bmj.com | link-loop | 100354
+ www.researchgate.net | redirect-loop | 84366
+ www.cambridge.org | link-loop | 83171
+ jamanetwork.com | no-pdf-link | 75053
+ febs.onlinelibrary.wiley.com | no-pdf-link | 74872
+ www.jstor.org | redirect-loop | 72059
+ journals.sagepub.com | no-pdf-link | 63028
+ science.sciencemag.org | redirect-loop | 62927
+ profile.thieme.de | no-pdf-link | 62406
+ cyberleninka.ru | redirect-loop | 56733
+ link.springer.com | link-loop | 47608
+ physoc.onlinelibrary.wiley.com | no-pdf-link | 30180
+ science.sciencemag.org | link-loop | 29908
+ papers.ssrn.com | redirect-loop | 27255
+ obgyn.onlinelibrary.wiley.com | no-pdf-link | 26789
+ www.computer.org | no-pdf-link | 26444
+ watermark.silverchair.com | terminal-bad-status | 25934
+ www.nature.com | redirect-loop | 25306
+ (30 rows)
diff --git a/notes/ingest/2020-03_s2_ingest.md b/notes/ingest/2020-03_s2.md
index fedaba0..fedaba0 100644
--- a/notes/ingest/2020-03_s2_ingest.md
+++ b/notes/ingest/2020-03_s2.md
diff --git a/notes/ingest/2020-04-07_datacite.md b/notes/ingest/2020-04-07_datacite.md
deleted file mode 100644
index b0217f0..0000000
--- a/notes/ingest/2020-04-07_datacite.md
+++ /dev/null
@@ -1,18 +0,0 @@
-
-After the broad datacite crawl, want to ingest paper PDFs into fatcat. But many
-of the DOIs are for, eg, datasets, and don't want to waste time on those.
-
-Instead of using full ingest request file from the crawl, will generate a new
-ingest request file using `fatcat_ingest.py` and set that up for bulk crawling.
-
-## Generate Requests
-
- ./fatcat_ingest.py --allow-non-oa --release-types article-journal,paper-conference,article,report,thesis,book,chapter query "doi_registrar:datacite" | pv -l > /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json
- => Expecting 8905453 release objects in search queries
- => 8.91M 11:49:50 [ 209 /s]
- => Counter({'elasticsearch_release': 8905453, 'ingest_request': 8905453, 'estimate': 8905453})
-
-## Bulk Ingest
-
- cat /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
-
diff --git a/notes/ingest/2020-04-07_unpaywall.md b/notes/ingest/2020-04-07_unpaywall.md
deleted file mode 100644
index e30d482..0000000
--- a/notes/ingest/2020-04-07_unpaywall.md
+++ /dev/null
@@ -1,63 +0,0 @@
-
-A new snapshot was released in April 2020 (the snapshot is from 2020-02-25, but
-not released for more than a month).
-
-Primary goal is:
-
-- generate ingest requests for only *new* URLs
-- bulk ingest these new URLs
-- crawl any no-capture URLs from that batch
-- re-bulk-ingest the no-capture batch
-- analytics on failed ingests. eg, any particular domains that are failing to crawl
-
-This ingest pipeline was started on 2020-04-07 by bnewbold.
-
-## Transform and Load
-
- # in sandcrawler pipenv on aitio
- zcat /schnell/UNPAYWALL-PDF-CRAWL-2020-04/unpaywall_snapshot_2020-02-25T115244.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json
- => 24.7M 5:17:03 [ 1.3k/s]
-
- cat /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
- => 24.7M
- => Worker: Counter({'total': 24712947, 'insert-requests': 4282167, 'update-requests': 0})
-
-## Dump new URLs and 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) > '2020-04-01'
- AND ingest_file_result.status IS NULL
- ) TO '/grande/snapshots/unpaywall_noingest_2020-04-08.rows.json';
- => 3696189
-
- cat /grande/snapshots/unpaywall_noingest_2020-04-08.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
-
-## Dump no-capture
-
- 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) > '2020-04-01'
- AND ingest_file_result.status = 'no-capture'
- 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%'
- ) TO '/grande/snapshots/unpaywall_nocapture_2020-04-XX.rows.json';
diff --git a/notes/ingest/2020-04_datacite.md b/notes/ingest/2020-04_datacite.md
new file mode 100644
index 0000000..0fc7e67
--- /dev/null
+++ b/notes/ingest/2020-04_datacite.md
@@ -0,0 +1,121 @@
+
+After the broad datacite crawl, want to ingest paper PDFs into fatcat. But many
+of the DOIs are for, eg, datasets, and don't want to waste time on those.
+
+Instead of using full ingest request file from the crawl, will generate a new
+ingest request file using `fatcat_ingest.py` and set that up for bulk crawling.
+
+## Generate Requests
+
+ ./fatcat_ingest.py --allow-non-oa --release-types article-journal,paper-conference,article,report,thesis,book,chapter query "doi_registrar:datacite" | pv -l > /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json
+ => Expecting 8905453 release objects in search queries
+ => 8.91M 11:49:50 [ 209 /s]
+ => Counter({'elasticsearch_release': 8905453, 'ingest_request': 8905453, 'estimate': 8905453})
+
+## Bulk Ingest
+
+ cat /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+## Ingest Stats
+
+Note that this will have a small fraction of non-datacite results mixed in (eg,
+from COVID-19 targeted crawls):
+
+ 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_type = 'pdf'
+ AND ingest_request.ingest_request_source = 'fatcat-ingest'
+ AND created >= '2020-04-07'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------------------+---------
+ no-pdf-link | 4646767
+ redirect-loop | 1447229
+ no-capture | 860235
+ success | 849501
+ terminal-bad-status | 174869
+ cdx-error | 159805
+ wayback-error | 18076
+ wrong-mimetype | 11169
+ link-loop | 8410
+ gateway-timeout | 4034
+ spn2-cdx-lookup-failure | 510
+ petabox-error | 339
+ null-body | 251
+ spn2-error | 19
+ spn2-error:job-failed | 14
+ bad-gzip-encoding | 13
+ timeout | 5
+ spn2-error:soft-time-limit-exceeded | 4
+ invalid-host-resolution | 2
+ spn2-error:pending | 1
+ (20 rows)
+
+Top domains/statuses (including success):
+
+ SELECT domain, status, COUNT((domain, status))
+ FROM (
+ SELECT
+ ingest_file_result.ingest_type,
+ ingest_file_result.status,
+ substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain
+ FROM ingest_file_result
+ LEFT JOIN ingest_request
+ 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_type = 'pdf'
+ AND ingest_request.ingest_request_source = 'fatcat-ingest'
+ AND created >= '2020-04-07'
+ ) t1
+ WHERE t1.domain != ''
+ AND t1.status != 'success'
+ GROUP BY domain, status
+ ORDER BY COUNT DESC
+ LIMIT 30;
+
+ domain | status | count
+ ---------------------------------------+---------------------+--------
+ ssl.fao.org | no-pdf-link | 862277
+ www.e-periodica.ch | no-pdf-link | 746781
+ www.researchgate.net | redirect-loop | 664524
+ dlc.library.columbia.edu | no-pdf-link | 493111
+ www.die-bonn.de | redirect-loop | 352903
+ figshare.com | no-pdf-link | 319709
+ statisticaldatasets.data-planet.com | no-pdf-link | 309584
+ catalog.paradisec.org.au | redirect-loop | 225396
+ zenodo.org | no-capture | 193201
+ digi.ub.uni-heidelberg.de | no-pdf-link | 184974
+ open.library.ubc.ca | no-pdf-link | 167841
+ zenodo.org | no-pdf-link | 130617
+ www.google.com | no-pdf-link | 111312
+ www.e-manuscripta.ch | no-pdf-link | 79192
+ ds.iris.edu | no-pdf-link | 77649
+ data.inra.fr | no-pdf-link | 69440
+ www.tib.eu | no-pdf-link | 63872
+ www.egms.de | redirect-loop | 53877
+ archaeologydataservice.ac.uk | redirect-loop | 52838
+ d.lib.msu.edu | no-pdf-link | 45297
+ www.e-rara.ch | no-pdf-link | 45163
+ springernature.figshare.com | no-pdf-link | 42527
+ boris.unibe.ch | no-pdf-link | 40816
+ www.research-collection.ethz.ch | no-capture | 40350
+ spectradspace.lib.imperial.ac.uk:8443 | no-pdf-link | 33059
+ repository.dri.ie | terminal-bad-status | 32760
+ othes.univie.ac.at | no-pdf-link | 32558
+ repositories.lib.utexas.edu | no-capture | 31526
+ posterng.netkey.at | no-pdf-link | 30315
+ zenodo.org | terminal-bad-status | 29614
+ (30 rows)
+
diff --git a/notes/ingest/2020-04_unpaywall.md b/notes/ingest/2020-04_unpaywall.md
new file mode 100644
index 0000000..bce757b
--- /dev/null
+++ b/notes/ingest/2020-04_unpaywall.md
@@ -0,0 +1,129 @@
+
+A new snapshot was released in April 2020 (the snapshot is from 2020-02-25, but
+not released for more than a month).
+
+Primary goal is:
+
+- generate ingest requests for only *new* URLs
+- bulk ingest these new URLs
+- crawl any no-capture URLs from that batch
+- re-bulk-ingest the no-capture batch
+- analytics on failed ingests. eg, any particular domains that are failing to crawl
+
+This ingest pipeline was started on 2020-04-07 by bnewbold.
+
+Ran through the first two steps again on 2020-05-03 after unpaywall had
+released another dump (dated 2020-04-27).
+
+## Transform and Load
+
+ # in sandcrawler pipenv on aitio
+ zcat /schnell/UNPAYWALL-PDF-CRAWL-2020-04/unpaywall_snapshot_2020-02-25T115244.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json
+ => 24.7M 5:17:03 [ 1.3k/s]
+
+ cat /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
+ => 24.7M
+ => Worker: Counter({'total': 24712947, 'insert-requests': 4282167, 'update-requests': 0})
+
+Second time:
+
+ # in sandcrawler pipenv on aitio
+ zcat /schnell/UNPAYWALL-PDF-CRAWL-2020-04/unpaywall_snapshot_2020-04-27T153236.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-04-27.ingest_request.json
+ => 25.2M 3:16:28 [2.14k/s]
+
+ cat /grande/snapshots/unpaywall_snapshot_2020-04-27.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
+ => Worker: Counter({'total': 25189390, 'insert-requests': 1408915, 'update-requests': 0})
+ => JSON lines pushed: Counter({'pushed': 25189390, 'total': 25189390})
+
+
+## Dump new URLs and 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) > '2020-04-01'
+ AND ingest_file_result.status IS NULL
+ ) TO '/grande/snapshots/unpaywall_noingest_2020-04-08.rows.json';
+ => 3696189
+
+ cat /grande/snapshots/unpaywall_noingest_2020-04-08.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+Second time:
+
+ 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) > '2020-05-01'
+ AND ingest_file_result.status IS NULL
+ ) TO '/grande/snapshots/unpaywall_noingest_2020-05-03.rows.json';
+ => 1799760
+
+ cat /grande/snapshots/unpaywall_noingest_2020-05-03.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+## Dump no-capture, Run Crawl
+
+Make two ingest request dumps: one with "all" URLs, which we will have heritrix
+attempt to crawl, and then one with certain domains filtered out, which we may
+or may not bother trying to ingest (due to expectation of failure).
+
+ 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) > '2020-04-01'
+ AND ingest_file_result.status = 'no-capture'
+ ) TO '/grande/snapshots/unpaywall_nocapture_all_2020-05-04.rows.json';
+ => 2734145
+
+ 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) > '2020-04-01'
+ AND ingest_file_result.status = 'no-capture'
+ 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%'
+ ) TO '/grande/snapshots/unpaywall_nocapture_2020-05-04.rows.json';
+ => 2602408
+
+Not actually a very significant size difference after all.
+
+See `journal-crawls` repo for details on seedlist generation and crawling.
+
+## Re-Ingest Post-Crawl
+
+Test small batch:
+
+ zcat /grande/snapshots/unpaywall_nocapture_all_2020-05-04.rows.json.gz | head -n200 | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+Run the whole batch:
+
+ zcat /grande/snapshots/unpaywall_nocapture_all_2020-05-04.rows.json.gz | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
diff --git a/notes/ingest/2020-05_oai_pmh.md b/notes/ingest/2020-05_oai_pmh.md
new file mode 100644
index 0000000..4cfd8d5
--- /dev/null
+++ b/notes/ingest/2020-05_oai_pmh.md
@@ -0,0 +1,125 @@
+
+Primary Goal: start large crawl of OAI landing pages that we haven't seen
+
+Fields of interest for ingest:
+- oai identifer
+- doi
+- formats
+- urls (maybe also "relations")
+- types (type+stage)
+
+## Other Tasks
+
+About 150 million total lines.
+
+Types coverage
+
+ zstdcat oai.ndjson.zst | pv -l | jq "select(.types != null) | .types[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > types_counts.txt
+
+Dump all ISSNs, with counts, quick check how many are in chocula/fatcat
+
+ zstdcat oai.ndjson.zst | pv -l | jq "select(.issn != null) | .issn[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > issn_counts.txt
+
+Language coverage
+
+ zstdcat oai.ndjson.zst | pv -l | jq "select(.languages != null) | .languages[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > languages_counts.txt
+
+Format coverage
+
+ zstdcat oai.ndjson.zst | pv -l | jq "select(.formats != null) | .formats[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > formats_counts.txt
+ => 150M 0:56:14 [44.7k/s]
+
+Have a DOI?
+
+ zstdcat oai.ndjson.zst | pv -l | rg '"doi":' | rg '"10.' | wc -l
+ => 16,013,503
+
+ zstdcat oai.ndjson.zst | pv -l | jq "select(.doi != null) | .doi[]" -r | sort -u -S 5G > doi_raw.txt
+ => 11,940,950
+
+## Transform, Load, Bulk Ingest
+
+ zstdcat oai.ndjson.zst | ./oai2ingestrequest.py - | pv -l | gzip > oai.202002.requests.json.gz
+ => 80M 6:36:55 [3.36k/s]
+
+ time zcat /schnell/oai-pmh/oai.202002.requests.json.gz | pv -l | ./persist_tool.py ingest-request -
+ => 80M 4:00:21 [5.55k/s]
+ => Worker: Counter({'total': 80013963, 'insert-requests': 51169081, 'update-requests': 0})
+ => JSON lines pushed: Counter({'pushed': 80013963, 'total': 80013963})
+
+ => real 240m21.207s
+ => user 85m12.576s
+ => sys 3m29.580s
+
+ select count(*) from ingest_request where ingest_type = 'pdf' and link_source = 'oai';
+ => 51,185,088
+
+Why so many (30 million) skipped? Not unique?
+
+ zcat oai.202002.requests.json.gz | jq '[.link_source_id, .base_url]' -c | sort -u -S 4G | wc -l
+ => 51,185,088
+
+ zcat oai.202002.requests.json.gz | jq .base_url -r | pv -l | sort -u -S 4G > request_url.txt
+ wc -l request_url.txt
+ => 50,002,674 request_url.txt
+
+ zcat oai.202002.requests.json.gz | jq .link_source_id -r | pv -l | sort -u -S 4G > requires_oai.txt
+ wc -l requires_oai.txt
+ => 34,622,083 requires_oai.txt
+
+Yup, tons of duplication. And remember this is exact URL, not SURT or similar.
+
+How many of these are URLs we have seen and ingested already?
+
+ 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'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+ status | count
+ -------------------------+----------
+ | 49491452
+ success | 1469113
+ no-capture | 134611
+ redirect-loop | 59666
+ no-pdf-link | 8947
+ cdx-error | 7561
+ terminal-bad-status | 6704
+ null-body | 5042
+ wrong-mimetype | 879
+ wayback-error | 722
+ petabox-error | 198
+ gateway-timeout | 86
+ link-loop | 51
+ invalid-host-resolution | 24
+ spn2-cdx-lookup-failure | 22
+ spn2-error | 4
+ bad-gzip-encoding | 4
+ spn2-error:job-failed | 2
+ (18 rows)
+
+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_request.link_source = 'oai'
+ AND date(ingest_request.created) > '2020-05-01'
+ AND ingest_file_result.status IS NULL
+ ) TO '/grande/snapshots/oai_noingest_20200506.requests.json';
+ => COPY 49491452
+
+ cat /grande/snapshots/oai_noingest_20200506.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
diff --git a/notes/ingest/NEXT.md b/notes/ingest/NEXT.md
new file mode 100644
index 0000000..8cdd6df
--- /dev/null
+++ b/notes/ingest/NEXT.md
@@ -0,0 +1,52 @@
+
+biorxiv
+medrxiv
+ doi:10.1101\/20*
+
+persee.fr 147k
+ publisher:persee in_ia:false is_oa:true
+ https://www.persee.fr/doc/pumus_1164-5385_1992_num_2_1_1013
+
+cairn.info: 161k
+ doi_prefix:10.3917 in_ia:false is_oa:true
+ https://www.cairn.info/revue-afrique-contemporaine-2011-3-page-161.htm
+ https://www.cairn.info/revue-cahiers-de-psychologie-clinique-2014-1-page-209.htm
+
+IOP OA: 169k
+ doi_prefix:10.1088 is_oa:true in_ia:false
+
+indian journals platform? 124k
+ doi_prefix:10.4103 in_ia:false is_oa:true
+ http://www.urologyannals.com/article.asp?issn=0974-7796;year=2011;volume=3;issue=3;spage=138;epage=140;aulast=Ahmad
+ http://www.neurologyindia.com/article.asp?issn=0028-3886;year=2011;volume=59;issue=4;spage=612;epage=615;aulast=Utsuki
+
+openedition? 48k
+ doi_prefix:10.4000 is_oa:true in_ia:false
+
+german medical science (GMS) 28k
+ doi_prefix:10.3205 in_ia:false is_oa:true
+ https://www.egms.de/static/en/journals/zma/2015-32/zma000965.shtml
+
+siberian chemistry 28k
+ doi_prefix:10.2298 in_ia:false is_oa:true
+ http://www.doiserbia.nb.rs/Article.aspx?ID=0352-51391000105H
+
+jalc oa doi: 82k
+ doi_registrar:jalc in_ia:false is_oa:true
+
+sage OA papers
+ https://journals.sagepub.com/doi/10.1177/034003529802400510
+
+Scientific Reports: 25k
+ in_ia:false container_id:"tnqhc2x2aneavcd3gx5h7mswhm"
+
+U Toronto press: 23k
+ publisher:"Toronto Press" in_ia:false is_oa:true
+ has an annoying bounce page
+
+ASHA (speech-language-hearing association): 7k
+ publisher:Speech-Language-Hearing in_ia:false is_oa:true
+
+MIT press journals
+
+
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-23 18:39:14 +0000