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|
This is the first ingest (and crawl) of URLs from DOAJ article-level metadata.
It will include at least 'pdf' and 'html' ingest requests, not just 'pdf' as in
the past.
Working off a 2020-11-13 snapshot.
## Transform and Load
# in sandcrawler pipenv on aitio
zcat /schnell/DOAJ-CRAWL-2020-11/doaj_article_data_2020-11-13_all.json.gz | ./scripts/doaj2ingestrequest.py - | pv -l > /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json
=> 6.7M 0:24:28 [4.57k/s]
cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
=> ran in to error with blank `base_url`
Second try after patches:
zcat /schnell/DOAJ-CRAWL-2020-11/doaj_article_data_2020-11-13_all.json.gz | ./scripts/doaj2ingestrequest.py - | pv -l > /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json
=> 6.7M 0:24:29 [4.56k/s]
cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | pv -l | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 6703036, 'insert-requests': 163854, 'update-requests': 0})
=> JSON lines pushed: Counter({'total': 6703036, 'pushed': 6703036})
## Check Pre-Crawl Status
SELECT ingest_request.ingest_type, 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.link_source = 'doaj'
GROUP BY ingest_request.ingest_type, status
-- next time include ingest_type in sort
ORDER BY COUNT DESC
LIMIT 30;
ingest_type | status | count
-------------+-------------------------+---------
pdf | | 3711532
html | | 2429003
pdf | success | 454403
pdf | redirect-loop | 48587
pdf | no-pdf-link | 24901
pdf | no-capture | 11569
xml | | 9442
pdf | link-loop | 8466
pdf | terminal-bad-status | 2015
pdf | wrong-mimetype | 1441
pdf | null-body | 1057
pdf | petabox-error | 299
pdf | cdx-error | 124
pdf | gateway-timeout | 114
pdf | wayback-error | 77
pdf | spn2-cdx-lookup-failure | 20
pdf | invalid-host-resolution | 4
pdf | spn2-error | 1
(18 rows)
## Dump new URLs, Transform, Bulk Ingest (PDF and XML only)
Dump:
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
AND ingest_file_result.ingest_type = ingest_request.ingest_type
WHERE
(ingest_request.ingest_type = 'pdf'
OR ingest_request.ingest_type = 'xml')
AND ingest_request.link_source = 'doaj'
-- AND date(ingest_request.created) > '2020-12-01'
AND (ingest_file_result.status IS NULL
OR ingest_file_result.status = 'no-capture')
) TO '/grande/snapshots/doaj_noingest_2020-11-19.rows.json';
=> COPY 3732543
Transform:
./scripts/ingestrequest_row2json.py /grande/snapshots/doaj_noingest_2020-11-19.rows.json | pv -l | shuf > /grande/snapshots/doaj_noingest_2020-11-19.ingest_request.json
=> 3.73M 0:02:18 [26.9k/s]
Definitely some non-URL strings in there; should try to filter those out
earlier in the transform process. And/or have a constraint on the URL column in
the database.
Enqueue the whole batch:
cat /grande/snapshots/doaj_noingest_2020-11-19.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Started this batch off at 2020-11-19 18:10 (Pacific time)
Stats after run:
SELECT ingest_request.ingest_type, 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.link_source = 'doaj'
GROUP BY ingest_request.ingest_type, status
ORDER BY ingest_request.ingest_type, COUNT DESC
LIMIT 30;
## Dump Seedlist
After preliminary bulk ingest attempts, dump rows:
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.base_url = ingest_request.base_url
AND ingest_file_result.ingest_type = ingest_request.ingest_type
WHERE
ingest_request.link_source = 'doaj'
AND (ingest_request.ingest_type = 'pdf'
OR ingest_request.ingest_type = 'xml')
AND ingest_file_result.status != 'success'
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 '%://web.archive.org/%'
AND ingest_request.base_url NOT LIKE '%://www.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 '%://web.archive.org/%'
AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%'
) t1
) TO '/grande/snapshots/doaj_seedlist_2020-11-19.rows.json';
=> 1,899,555
TODO: filter for valid URLs
Prep ingest requests (for post-crawl use):
./scripts/ingestrequest_row2json.py /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | pv -l > /grande/snapshots/doaj_crawl_ingest_2020-11-19.json
And actually dump seedlist(s):
cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | jq -r .base_url | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.url.txt
cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.terminal_url.txt
cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.no_terminal_url.txt
wc -l doaj_seedlist_2020-11-19.*.txt
## Post-Crawl Ingest
Re-run all ingests, from original batch (pdf, xml, and html), now that DOAJ
identifiers are all in fatcat:
cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
# started 2020-12-23 15:05 (Pacific)
# finished around 2020-12-31, after one long/slow partition
Stats again after everything:
SELECT ingest_request.ingest_type, 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.link_source = 'doaj'
GROUP BY ingest_request.ingest_type, status
ORDER BY ingest_request.ingest_type, COUNT DESC
LIMIT 50;
ingest_type | status | count
-------------+--------------------------+---------
html | wrong-scope | 1089423
html | no-capture | 423917
html | redirect-loop | 212910
html | unknown-scope | 204069
html | html-resource-no-capture | 165587
html | success | 122937
html | null-body | 100296
html | wayback-content-error | 53918
html | wrong-mimetype | 18908
html | terminal-bad-status | 14059
html | petabox-error | 13520
html | cdx-error | 6823
html | wayback-error | 890
html | | 620
html | blocked-cookie | 543
html | blocked-captcha | 250
html | redirects-exceeded | 135
html | too-many-resources | 111
html | max-hops-exceeded | 84
html | bad-redirect | 3
pdf | success | 2851324
pdf | no-pdf-link | 529914
pdf | redirect-loop | 349494
pdf | no-capture | 272202
pdf | null-body | 129027
pdf | terminal-bad-status | 91796
pdf | link-loop | 25267
pdf | wrong-mimetype | 6504
pdf | wayback-error | 2968
pdf | | 2068
pdf | wayback-content-error | 1548
pdf | cdx-error | 1095
pdf | petabox-error | 1024
pdf | bad-redirect | 203
pdf | redirects-exceeded | 135
pdf | timeout | 20
pdf | max-hops-exceeded | 19
pdf | bad-gzip-encoding | 2
xml | success | 6897
xml | null-body | 2353
xml | wrong-mimetype | 184
xml | no-capture | 5
xml | cdx-error | 3
(43 rows)
And on filtered subset that we actually crawled:
SELECT ingest_request.ingest_type, 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.link_source = 'doaj'
AND (ingest_request.ingest_type = 'pdf'
OR ingest_request.ingest_type = 'xml')
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 '%://web.archive.org/%'
AND ingest_request.base_url NOT LIKE '%://www.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 '%://web.archive.org/%'
AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%'
GROUP BY ingest_request.ingest_type, status
ORDER BY ingest_request.ingest_type, COUNT DESC
LIMIT 50;
ingest_type | status | count
-------------+-----------------------+---------
pdf | success | 2851286
pdf | no-pdf-link | 527495
pdf | redirect-loop | 345138
pdf | no-capture | 268140
pdf | null-body | 129027
pdf | terminal-bad-status | 91125
pdf | link-loop | 25267
pdf | wrong-mimetype | 6504
pdf | wayback-error | 2907
pdf | petabox-error | 363
pdf | wayback-content-error | 242
pdf | bad-redirect | 203
pdf | redirects-exceeded | 135
pdf | max-hops-exceeded | 19
pdf | cdx-error | 15
pdf | bad-gzip-encoding | 2
xml | success | 6897
xml | null-body | 2353
xml | wrong-mimetype | 184
xml | no-capture | 5
(20 rows)
|
