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|
Using 2020-06-25 upstream MAG corpus snapshot.
Ran munging from `scratch:ingest/mag` notes first.
Expecting a couple million new ingest request URLs; this is the first "patch"
MAG ingest on top of existing already-run requests.
Planning to skip the initial bulk ingest step, on the assumption that new URLs
have either been ingested already (eg, via continuous ingest pipeline) or need
crawling.
## Generate Requests
export LC_ALL=C
cat PaperUrls_mag_url_doi.all.txt | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-06-25 | pv -l > ingest_requests_mag-2020-06-25.json
=> 28.7M 2:36:48 [3.06k/s]
export LC_ALL=C
zcat PaperUrls_mag_url_pmid.txt.gz | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-06-25 --pmid | pv -l > ingest_requests_mag-2020-06-25.pmid.json
=> 5.66M 0:29:28 [ 3.2k/s]
## Persist Ingest Requests
# small sample
head -n1000 /schnell/mag/20200625/ingest_requests_mag-2020-06-25.pmid.json | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 1000, 'insert-requests': 319, 'update-requests': 0})
head -n1000 /schnell/mag/20200625/ingest_requests_mag-2020-06-25.json | ./persist_tool.py ingest-request -
Worker: Counter({'total': 1000, 'insert-requests': 304, 'update-requests': 0})
cat /schnell/mag/20200625/ingest_requests_mag-2020-06-25.pmid.json | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 5662486, 'insert-requests': 1984605, 'update-requests': 0})
cat /schnell/mag/20200625/ingest_requests_mag-2020-06-25.json | ./persist_tool.py ingest-request -
=> Worker: Counter({'total': 28743819, 'insert-requests': 7433465, 'update-requests': 0})
## Crawl/Dupe Status
Overall status for old and new seeds, filtering out large (blocking)
publishers:
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'
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%'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+----------
success | 19477651
| 8238898
redirect-loop | 2036494
link-loop | 1330036
no-pdf-link | 1304820
terminal-bad-status | 648150
no-capture | 545785
gateway-timeout | 200143
cdx-error | 149995
spn2-cdx-lookup-failure | 80010
wrong-mimetype | 57052
wayback-error | 41032
invalid-host-resolution | 37203
petabox-error | 11167
null-body | 6662
spn2-error | 1698
spn2-error:job-failed | 775
spn2-error:invalid-url-syntax | 335
spn2-error:soft-time-limit-exceeded | 191
bad-redirect | 77
(20 rows)
Just the new seeds:
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'
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.created > '2020-06-20'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+---------
| 8238851
success | 787174
no-capture | 42864
redirect-loop | 31718
terminal-bad-status | 31493
no-pdf-link | 13025
cdx-error | 11275
wrong-mimetype | 6238
link-loop | 3365
wayback-error | 748
gateway-timeout | 506
null-body | 191
spn2-cdx-lookup-failure | 99
petabox-error | 89
invalid-host-resolution | 70
spn2-error | 7
spn2-error:job-failed | 2
spn2-error:soft-time-limit-exceeded | 1
bad-gzip-encoding | 1
(19 rows)
Where are no-capture results terminating? May need to add or update heritrix
crawl config so that we get better yield without needing to do SPNv2 crawling.
SELECT initial_domain, terminal_domain, COUNT(*)
FROM (
SELECT
ingest_file_result.status as status,
substring(ingest_file_result.base_url FROM '[^/]+://([^/]*)') AS initial_domain,
substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS terminal_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 = 'mag'
AND ingest_file_result.status = 'no-capture'
) t1
GROUP BY initial_domain, terminal_domain
ORDER BY COUNT DESC
LIMIT 25;
initial_domain | terminal_domain | count
---------------------------------+---------------------+--------
www.researchgate.net | | 334145
academic.oup.com | | 205820
www.tandfonline.com | | 148638
journals.sagepub.com | | 144196
muse.jhu.edu | | 55957
hrcak.srce.hr | | 25317
www.omicsonline.org | | 22426
link.springer.com | | 21044
iopscience.iop.org | | 12385
bioone.org | | 9097
tandfonline.com | | 8512
or.nsfc.gov.cn | | 4823
ieeexplore.ieee.org | ieeexplore.ieee.org | 4398
pubs.acs.org | | 3708
archive-ouverte.unige.ch | | 2743
dergipark.ulakbim.gov.tr | | 2677
hal.archives-ouvertes.fr | | 1258
dergipark.org.tr | | 1207
apo.org.au | | 1186
spire.sciencespo.fr | | 989
cyberleninka.ru | | 895
lirias.kuleuven.be | | 855
tel.archives-ouvertes.fr | | 786
pub.uni-bielefeld.de | | 728
www.research-collection.ethz.ch | | 670
(25 rows)
## Heritrix Seedlist Generation
Dump ingest requests (filtered for some domains that don't expect to crawl via
heritrix):
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'
OR ingest_file_result.status IS NULL)
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_20200708.rows.json';
=> 8784683
# in sandcrawler pipenv
./scripts/ingestrequest_row2json.py /grande/snapshots/mag_nocapture_20200708.rows.json > /grande/snapshots/mag_nocapture_20200708.json
Seedlist transform from here on covered in MAG crawl notes.
## Bulk Ingest
Run ingest requests on everything we crawled:
cat /grande/snapshots/mag_nocapture_20200708.json | | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Small sample:
head -n1000 /grande/snapshots/mag_nocapture_20200708.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
Full run:
cat /grande/snapshots/mag_nocapture_20200708.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1
## Updated Overall 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 = 'mag'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+----------
success | 24574294
redirect-loop | 2633731
no-capture | 2458694
no-pdf-link | 1896871
link-loop | 1510899
terminal-bad-status | 878821
cdx-error | 387574
gateway-timeout | 200246
| 170304
wayback-error | 97572
spn2-cdx-lookup-failure | 80284
wrong-mimetype | 65097
invalid-host-resolution | 37204
petabox-error | 12097
null-body | 8549
spn2-error | 1706
spn2-error:job-failed | 775
spn2-error:invalid-url-syntax | 335
spn2-error:soft-time-limit-exceeded | 191
bad-redirect | 90
(20 rows)
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'
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%'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+----------
success | 24557382
redirect-loop | 2630582
no-capture | 1947066
no-pdf-link | 1778206
link-loop | 1510790
terminal-bad-status | 857173
cdx-error | 384525
gateway-timeout | 200143
wayback-error | 96390
spn2-cdx-lookup-failure | 80010
wrong-mimetype | 64908
invalid-host-resolution | 37203
petabox-error | 12087
null-body | 8548
spn2-error | 1698
spn2-error:job-failed | 775
spn2-error:invalid-url-syntax | 335
spn2-error:soft-time-limit-exceeded | 191
bad-redirect | 90
| 69
(20 rows)
Just the new seeds:
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'
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.created > '2020-06-20'
GROUP BY status
ORDER BY COUNT DESC
LIMIT 20;
status | count
-------------------------------------+---------
success | 5860601
no-capture | 1489959
redirect-loop | 619121
no-pdf-link | 473703
terminal-bad-status | 234753
cdx-error | 231575
link-loop | 184093
wayback-error | 56068
wrong-mimetype | 14046
null-body | 2068
petabox-error | 1006
gateway-timeout | 506
spn2-cdx-lookup-failure | 99
invalid-host-resolution | 70
| 22
bad-redirect | 13
spn2-error | 7
timeout | 3
spn2-error:job-failed | 2
spn2-error:soft-time-limit-exceeded | 1
(20 rows)
|
