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|
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
WARNING: forgot to transform from rows to ingest requests.
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
WARNING: forgot to transform from rows to ingest requests.
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
NOTE: forgot here to transform from "rows" to ingest requests.
Not actually a very significant size difference after all.
See `journal-crawls` repo for details on seedlist generation and crawling.
## Re-Ingest Post-Crawl
NOTE: if we *do* want to do cleanup eventually, could look for fatcat edits
between 2020-04-01 and 2020-05-25 which have limited "extra" metadata (eg, no
evidence or `oa_status`).
The earlier bulk ingests were done wrong (forgot to transform from rows to full
ingest request docs), so going to re-do those, which should be a superset of
the nocapture crawl URLs.:
./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_noingest_2020-04-08.rows.json | pv -l > /grande/snapshots/unpaywall_noingest_2020-04-08.json
=> 1.26M 0:00:58 [21.5k/s]
=> previously: 3,696,189
./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_noingest_2020-05-03.rows.json | pv -l > /grande/snapshots/unpaywall_noingest_2020-05-03.json
=> 1.26M 0:00:56 [22.3k/s]
Crap, looks like the 2020-04-08 segment got overwriten with 2020-05 data by
accident. Hrm... need to re-ingest *all* recent unpaywall URLs:
COPY (
SELECT row_to_json(ingest_request.*)
FROM ingest_request
WHERE
ingest_request.ingest_type = 'pdf'
AND ingest_request.link_source = 'unpaywall'
AND date(ingest_request.created) > '2020-04-01'
) TO '/grande/snapshots/unpaywall_all_recent_requests_2020-05-26.rows.json';
=> COPY 5691106
./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.rows.json | pv -l | shuf > /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json
=> 5.69M 0:04:26 [21.3k/s]
Start small:
cat /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json | head -n200 | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Looks good (whew), run the full thing:
cat /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
## Post-ingest stats (2020-08-28)
Overall status:
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'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+----------
success | 22063013
no-pdf-link | 2192606
redirect-loop | 1471135
terminal-bad-status | 995106
no-capture | 359440
cdx-error | 358909
wrong-mimetype | 111685
wayback-error | 50705
link-loop | 29359
null-body | 13667
gateway-timeout | 3689
spn2-cdx-lookup-failure | 1229
petabox-error | 1007
redirects-exceeded | 747
invalid-host-resolution | 464
spn2-error | 107
spn2-error:job-failed | 91
bad-redirect | 26
spn2-error:soft-time-limit-exceeded | 9
bad-gzip-encoding | 5
(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 = 'unpaywall'
) t1
WHERE t1.domain != ''
AND t1.status != 'success'
AND t1.status != 'no-capture'
GROUP BY domain, status
ORDER BY COUNT DESC
LIMIT 30;
domain | status | count
-----------------------------------+---------------------+--------
academic.oup.com | no-pdf-link | 415441
watermark.silverchair.com | terminal-bad-status | 345937
www.tandfonline.com | no-pdf-link | 262488
journals.sagepub.com | no-pdf-link | 235707
onlinelibrary.wiley.com | no-pdf-link | 225876
iopscience.iop.org | terminal-bad-status | 170783
www.nature.com | redirect-loop | 145522
www.degruyter.com | redirect-loop | 131898
files-journal-api.frontiersin.org | terminal-bad-status | 126091
pubs.acs.org | no-pdf-link | 119223
society.kisti.re.kr | no-pdf-link | 112401
www.ahajournals.org | no-pdf-link | 105953
dialnet.unirioja.es | terminal-bad-status | 96505
www.cell.com | redirect-loop | 87560
www.ncbi.nlm.nih.gov | redirect-loop | 49890
ageconsearch.umn.edu | redirect-loop | 45989
ashpublications.org | no-pdf-link | 45833
pure.mpg.de | redirect-loop | 45278
www.degruyter.com | terminal-bad-status | 43642
babel.hathitrust.org | terminal-bad-status | 42057
osf.io | redirect-loop | 41119
scialert.net | no-pdf-link | 39009
dialnet.unirioja.es | redirect-loop | 38839
www.jci.org | redirect-loop | 34209
www.spandidos-publications.com | redirect-loop | 33167
www.journal.csj.jp | no-pdf-link | 30915
journals.openedition.org | redirect-loop | 30409
www.valueinhealthjournal.com | redirect-loop | 30090
dergipark.org.tr | no-pdf-link | 29146
journals.ametsoc.org | no-pdf-link | 29133
(30 rows)
Enqueue internal failures for re-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 (
ingest_file_result.status = 'cdx-error' OR
ingest_file_result.status = 'wayback-error'
)
) TO '/grande/snapshots/unpaywall_errors_2020-08-28.rows.json';
|
