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. export SNAPSHOT=2022-03-09 export CRAWLVM=wbgrp-svc279.us.archive.org export CRAWLNAME=UNPAYWALL-CRAWL-2022-04 ## 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; status | count -------------------------+--------- no-capture | 3330232 success | 2455102 redirect-loop | 197117 terminal-bad-status | 82618 no-pdf-link | 33046 blocked-cookie | 16078 link-loop | 6745 wrong-mimetype | 3416 wayback-error | 1385 empty-blob | 1142 cdx-error | 820 body-too-large | 292 bad-gzip-encoding | 281 wayback-content-error | 267 | 253 petabox-error | 215 skip-url-blocklist | 185 null-body | 179 spn2-cdx-lookup-failure | 89 gateway-timeout | 73 (20 rows) After prior "TARGETED" crawl and bulk ingest finished: status | count -------------------------+--------- no-capture | 3330055 success | 2455279 redirect-loop | 197117 terminal-bad-status | 82618 no-pdf-link | 33046 blocked-cookie | 16079 link-loop | 6745 wrong-mimetype | 3416 wayback-error | 1385 empty-blob | 1142 cdx-error | 820 body-too-large | 292 bad-gzip-encoding | 281 wayback-content-error | 267 | 253 petabox-error | 215 skip-url-blocklist | 185 null-body | 179 spn2-cdx-lookup-failure | 89 gateway-timeout | 73 (20 rows) Almost no change, which makes sense because of the `ingest_request.created` filter. ## 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_request.base_url NOT LIKE '%://doi.org/10.48550/%' 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'; => before ingest and arxiv.org DOI exclusion: COPY 3309091 => COPY 3308914 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_$SNAPSHOT.json => 3.31M 0:02:22 [23.2k/s] And actually dump seedlist(s): cat /srv/sandcrawler/tasks/unpaywall_seedlist_$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_$SNAPSHOT.no_terminal_url.txt cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.no_terminal_url.txt /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.terminal_url.txt | awk '{print "F+ " $1}' | shuf > /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT* 15 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.no_terminal_url.txt 3308914 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.rows.json 3028879 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.terminal_url.txt 3038725 /srv/sandcrawler/tasks/unpaywall_seedlist_2022-03-09.url.txt Inject seedlist into crawler: scp /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule $CRAWLVM:/tmp ssh $CRAWLVM sudo -u heritrix cp /tmp/unpaywall_seedlist_$SNAPSHOT.schedule /0/ia-jobs/journal-crawls/$CRAWLNAME/action/ Top domains? cat /srv/sandcrawler/tasks/unpaywall_seedlist_$SNAPSHOT.schedule | cut -f2 -d' ' | cut -f3 -d/ | sort -S 4G | uniq -c | sort -nr | head -n20 158497 www.scielo.br 144732 onlinelibrary.wiley.com 129349 www.researchsquare.com 94923 hal.archives-ouvertes.fr 69293 openresearchlibrary.org 64584 www.cell.com 60033 link.springer.com 50528 www.degruyter.com 49737 projecteuclid.org 45841 www.jstage.jst.go.jp 44819 www.mdpi.com 44325 ieeexplore.ieee.org 38091 dr.lib.iastate.edu 31030 www.nature.com 30300 discovery.ucl.ac.uk 27692 ntrs.nasa.gov 24215 orca.cardiff.ac.uk 23653 www.frontiersin.org 23474 pure.rug.nl 22660 www.sciencedirect.com ## Post-Crawl bulk ingest # enqueue for bulk processing cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_$SNAPSHOT.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc350.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 # done: 2022-07-06 ## Post-Crawl, Post-Ingest Stats 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; status | count -------------------------+--------- success | 4784948 => +2,329,669 ~77% redirect-loop | 485270 => + 288,153 ~10% no-capture | 317598 => -3,012,457 terminal-bad-status | 267853 => + 185,235 ~ 6% no-pdf-link | 118303 => + 85,257 blocked-cookie | 111373 => + 95,294 skip-url-blocklist | 19368 link-loop | 9091 wrong-mimetype | 7163 cdx-error | 2516 empty-blob | 1961 wayback-error | 1922 body-too-large | 509 petabox-error | 416 wayback-content-error | 341 bad-gzip-encoding | 281 | 253 null-body | 179 spn2-cdx-lookup-failure | 89 gateway-timeout | 73 (20 rows) Groovy!