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-rw-r--r--notes/ingest/2022-04_targeted.md142
-rw-r--r--notes/ingest/2022-04_unpaywall.md135
2 files changed, 277 insertions, 0 deletions
diff --git a/notes/ingest/2022-04_targeted.md b/notes/ingest/2022-04_targeted.md
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+
+Want to do a crawl similar to recent "patch" crawls, where we run heritrix
+crawls to "fill in" missing (`no-capture`) and failed dailing ingests (aka,
+those requests coming from fatcat-changelog).
+
+ export PATCHDATE=2022-04-20
+ export CRAWLVM=wbgrp-svc279.us.archive.org
+ export CRAWLNAME=TARGETED-ARTICLE-CRAWL-2022-04
+
+## Seedlist Query
+
+Terminal URLs dump:
+
+ COPY (
+ SELECT row_to_json(t) FROM (
+ SELECT ingest_file_result.terminal_url, 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'
+ OR ingest_request.ingest_type = 'html'
+ )
+ -- AND ingest_file_result.updated >= '2022-01-12'
+ 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 LIKE 'spn2-%'
+ OR ingest_file_result.status = 'gateway-timeout'
+ OR (
+ ingest_file_result.status = 'terminal-bad-status'
+ AND (
+ ingest_file_result.terminal_status_code = 429
+ OR ingest_file_result.terminal_status_code = 500
+ OR ingest_file_result.terminal_status_code = 502
+ OR ingest_file_result.terminal_status_code = 503
+ )
+ )
+ )
+ AND (
+ ingest_request.link_source = 'doi'
+ OR ingest_request.link_source = 'arxiv'
+ OR ingest_request.link_source = 'doaj'
+ OR ingest_request.link_source = 'dblp'
+ OR ingest_request.link_source = 'pmc'
+ -- OR ingest_request.link_source = 'unpaywall'
+ -- OR ingest_request.link_source = 'oai'
+ )
+
+ 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%'
+ AND ingest_file_result.terminal_url NOT LIKE '%www.archive.org%'
+ ) t
+ ) TO '/srv/sandcrawler/tasks/patch_ingest_request_2022-04-20.rows.json';
+ # COPY 4842749
+
+ cat /srv/sandcrawler/tasks/patch_ingest_request_$PATCHDATE.rows.json \
+ | rg -v "\\\\" \
+ | jq -r .terminal_url \
+ | rg '://' \
+ | rg -i '^http' \
+ | rg -v www.archive.org \
+ | rg -v '://10\.' \
+ | rg -v '://172\.' \
+ | sort -u -S 4G \
+ | pv -l \
+ > /srv/sandcrawler/tasks/patch_terminal_url.$PATCHDATE.txt
+ # 4.75M 0:01:44 [45.4k/s]
+
+ # check top domains
+ cut -f3 -d/ /srv/sandcrawler/tasks/patch_terminal_url.$PATCHDATE.txt | sort | uniq -c | sort -nr | head -n25
+ 1515829 www.jstage.jst.go.jp
+ 1052953 doi.org
+ 241704 arxiv.org
+ 219543 www.sciencedirect.com
+ 178562 www.persee.fr
+ 84947 zenodo.org
+ 67397 www.mdpi.com
+ 65775 journals.lww.com
+ 58216 opg.optica.org
+ 50673 osf.io
+ 45776 www.degruyter.com
+ 36664 www.indianjournals.com
+ 35287 pubs.rsc.org
+ 33495 www.bmj.com
+ 33320 www.research-collection.ethz.ch
+ 29728 www.e-periodica.ch
+ 28338 iopscience.iop.org
+ 26364 www.cambridge.org
+ 23840 onlinelibrary.wiley.com
+ 23641 platform.almanhal.com
+ 22660 brill.com
+ 20288 www.osapublishing.org
+ 18561 cgscholar.com
+ 18539 doi.nrct.go.th
+ 15677 www.frontiersin.org
+
+ cat /srv/sandcrawler/tasks/patch_terminal_url.$PATCHDATE.txt | awk '{print "F+ " $1}' > /srv/sandcrawler/tasks/patch_terminal_url.$PATCHDATE.schedule
+
+ scp /srv/sandcrawler/tasks/patch_terminal_url.$PATCHDATE.schedule $CRAWLVM:/tmp
+ ssh $CRAWLVM sudo -u heritrix cp /tmp/patch_terminal_url.$PATCHDATE.schedule /0/ia-jobs/journal-crawls/$CRAWLNAME/action/
+
+TODO: starting with the "quarterly retry" script/query might make more sense?
+TODO: are there any cases where we do a bulk ingest request, fail, and `terminal_url` is not set?
+
+## Bulk Ingest Requests (post-crawl)
+
+ cd /srv/sandcrawler/src/python
+ sudo su sandcrawler
+ pipenv run ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/patch_ingest_request_$PATCHDATE.rows.json | pv -l > /srv/sandcrawler/tasks/patch_ingest_request_$PATCHDATE.ingest_request.json
+
+ cat /srv/sandcrawler/tasks/patch_ingest_request_$PATCHDATE.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/2022-04_unpaywall.md b/notes/ingest/2022-04_unpaywall.md
new file mode 100644
index 0000000..600b2d6
--- /dev/null
+++ b/notes/ingest/2022-04_unpaywall.md
@@ -0,0 +1,135 @@
+
+New unpaywall snapshot from `2022-03-09`.
+
+This will probably be the last unpaywall crawl? Will switch to openalex in the
+future, because we can automate that ingest process, and run it on our own
+schedule.
+
+## Download and Archive
+
+ wget 'https://unpaywall-data-snapshots.s3.us-west-2.amazonaws.com/unpaywall_snapshot_2022-03-09T083001.jsonl.gz'
+ # 2022-04-09 22:31:43 (98.9 KB/s) - ‘unpaywall_snapshot_2022-03-09T083001.jsonl.gz’ saved [29470830470/29470830470]
+
+ export SNAPSHOT=2022-03-09
+ ia upload unpaywall_snapshot_$SNAPSHOT unpaywall_snapshot_$SNAPSHOT*.jsonl.gz -m title:"Unpaywall Metadata Snapshot ($SNAPSHOT)" -m collection:ia_biblio_metadata -m creator:creator -m date:$SNAPSHOT
+
+ # if needed
+ scp unpaywall_snapshot_$SNAPSHOT*.jsonl.gz wbgrp-svc506.us.archive.org:/srv/sandcrawler/tasks
+
+## Transform and Load
+
+ # in sandcrawler pipenv on sandcrawler1-vm (svc506)
+ cd /srv/sandcrawler/src/python
+ sudo su sandcrawler
+ pipenv shell
+
+ zcat /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT*.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT.ingest_request.json
+ # 34.9M 3:02:32 [3.19k/s]
+
+ cat /srv/sandcrawler/tasks/unpaywall_snapshot_$SNAPSHOT.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
+ # 34.9M 5:23:15 [1.80k/s]
+ # Worker: Counter({'total': 34908779, 'insert-requests': 6129630, 'update-requests': 0})
+ # JSON lines pushed: Counter({'total': 34908779, 'pushed': 34908779})
+
+So about 6.1M new ingest request rows.
+
+## Dump new URLs, Transform, 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'
+ -- take "all time" instead of just this recent capture
+ -- AND date(ingest_request.created) > '2021-01-01'
+ AND (ingest_file_result.status IS NULL
+ OR ingest_file_result.status = 'no-capture')
+ ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2022-03-09.rows.json';
+ => COPY 6025671
+
+ # transform
+ ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.ingest_request.json
+ # 6.03M 0:03:26 [29.1k/s]
+
+ # enqueue for bulk processing
+ cat /srv/sandcrawler/tasks/unpaywall_noingest_$SNAPSHOT.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
+
+
+## Check Pre-Crawl Status
+
+Only the recent 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 = 'unpaywall'
+ AND date(ingest_request.created) > '2022-04-01'
+ GROUP BY status
+ ORDER BY COUNT DESC
+ LIMIT 20;
+
+
+## Dump Seedlist
+
+Dump rows for crawling:
+
+ 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 date(ingest_request.created) > '2022-04-01'
+ AND ingest_request.link_source = 'unpaywall'
+ 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 = 'gateway-timeout'
+ OR ingest_file_result.status LIKE 'spn2-%'
+ )
+ 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 '%.archive.org%'
+ AND ingest_request.base_url NOT LIKE '%://archive.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 '%.archive.org%'
+ AND ingest_file_result.terminal_url NOT LIKE '%://archive.org%'
+ ) t1
+ ) TO '/srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.rows.json';
+
+Prep ingest requests (for post-crawl use):
+
+ ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_$SNAPSHOT.json
+
+And actually dump seedlist(s):
+
+ cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.url.txt
+ cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.terminal_url.txt
+ cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.no_terminal_url.txt
+
+ wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.*.txt
+
+Then run crawl (see `journal-crawls` git repo), including frontier generation.
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-22 04:56:57 +0000