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|
## SQL Table Sizes
SELECT
table_name,
pg_size_pretty(table_size) AS table_size,
pg_size_pretty(indexes_size) AS indexes_size,
pg_size_pretty(total_size) AS total_size
FROM (
SELECT
table_name,
pg_table_size(table_name) AS table_size,
pg_indexes_size(table_name) AS indexes_size,
pg_total_relation_size(table_name) AS total_size
FROM (
SELECT ('"' || table_schema || '"."' || table_name || '"') AS table_name
FROM information_schema.tables
WHERE table_schema = 'public'
) AS all_tables
ORDER BY total_size DESC
) AS pretty_sizes;
table_name | table_size | indexes_size | total_size
-------------------------------+------------+--------------+------------
"public"."cdx" | 42 GB | 41 GB | 82 GB
"public"."grobid_shadow" | 64 GB | 6902 MB | 71 GB
"public"."grobid" | 59 GB | 7604 MB | 66 GB
"public"."file_meta" | 31 GB | 28 GB | 59 GB
"public"."ingest_request" | 19 GB | 20 GB | 39 GB
"public"."ingest_file_result" | 15 GB | 23 GB | 39 GB
"public"."shadow" | 9111 MB | 10204 MB | 19 GB
"public"."fatcat_file" | 5206 MB | 2094 MB | 7300 MB
"public"."pdftrio" | 618 MB | 432 MB | 1051 MB
"public"."petabox" | 403 MB | 594 MB | 997 MB
(10 rows)
Size: 383.93G
## File Metadata
Counts and total file size:
SELECT COUNT(*) as total_count, SUM(size_bytes) as total_size FROM file_meta;
total_count | total_size
-------------+-----------------
158059828 | 197346217653010
(1 row)
=> 158 million, 197 terabytes
Top mimetypes:
SELECT mimetype, COUNT(*) FROM file_meta GROUP BY mimetype ORDER BY COUNT DESC LIMIT 10;
mimetype | count
-------------------------------+-----------
application/pdf | 157805029
application/octet-stream | 154348
application/xml | 42170
text/html | 18703
text/plain | 15989
application/gzip | 6484
| 6040
application/postscript | 4912
application/vnd.ms-powerpoint | 1672
application/msword | 921
(10 rows)
Missing full metadata:
SELECT COUNT(*) FROM file_meta WHERE sha256hex IS NULL;
count
---------
1027125
(1 row)
## CDX
Total and unique-by-sha1 counts:
SELECT COUNT(DISTINCT sha1hex) as unique_sha1, COUNT(*) as total FROM cdx;
unique_sha1 | total
-------------+-----------
92936564 | 111022039
(1 row)
=> 110 million rows, 92.9 million files
mimetype counts:
SELECT mimetype, COUNT(*) FROM cdx GROUP BY mimetype ORDER BY COUNT(*) DESC LIMIT 25;
mimetype | count
---------------------------------------------------------------------------------------------------------+-----------
application/pdf | 104178718
warc/revisit | 5274410
text/xml | 519042
text/html | 295523
application/octet-stream | 259681
unk | 138930
application/postscript | 81065
application/save | 80765
binary/octet-stream | 59804
application/x-download | 27083
text/plain | 26938
application/download | 25125
image/pdf | 16095
application/force-download | 9004
application/x-msdownload | 3711
application | 2934
application/x-octetstream | 2926
multipart/form-data | 2741
application/x-pdf | 2444
.pdf | 2368
application/binary | 1268
application/pdf' | 1192
pdf | 1113
file/unknown | 1086
application/unknown | 761
file | 753
application/blob | 670
application/octetstream | 657
text/pdf | 549
0 | 417
('application/pdf', | 349
application/http;msgtype=response | 251
application/doc | 180
[...] (wasn't LIMIT 25)
Processed or not:
# TODO:
## GROBID
Counts:
SELECT COUNT(DISTINCT fatcat_release) AS unique_releases, COUNT(*) AS total FROM grobid;
unique_releases | total
-----------------+----------
17455441 | 92707544
(1 row)
Status?
SELECT status_code, COUNT(*) FROM grobid GROUP BY status_code ORDER BY COUNT DESC LIMIT 10;
What version used?
SELECT grobid_version, COUNT(*) FROM grobid WHERE status_code = 200 GROUP BY grobid_version ORDER BY COUNT DESC LIMIT 10;
grobid_version | count
----------------+----------
0.5.5-fatcat | 71057023
| 14638425
(2 rows)
SELECT grobid_version, COUNT(*) FROM grobid WHERE status = 'success' GROUP BY grobid_version ORDER BY COUNT DESC LIMIT 10;
grobid_version | count
----------------+----------
0.5.5-fatcat | 71057074
| 3
(2 rows)
## Petabox
Counts:
SELECT COUNT(DISTINCT sha1hex) as unique_sha1, COUNT(*) as total FROM petabox;
unique_sha1 | total
-------------+---------
2868825 | 2887834
## Ingests
Requests by source:
SELECT ingest_type, link_source, COUNT(*) FROM ingest_request GROUP BY ingest_type, link_source ORDER BY COUNT DESC LIMIT 25;
ingest_type | link_source | count
-------------+-----------------+----------
pdf | unpaywall | 26244088
pdf | mag | 25596658
pdf | doi | 15652966
pdf | pmc | 2043646
pdf | arxiv | 721902
pdf | cnki_covid19 | 2034
pdf | wanfang_covid19 | 975
pdf | spn | 103
SELECT ingest_type, link_source, ingest_request_source, COUNT(*) FROM ingest_request GROUP BY ingest_type, link_source, ingest_request_source ORDER BY COUNT DESC LIMIT 25;
ingest_type | link_source | ingest_request_source | count
-------------+-----------------+-------------------------+----------
pdf | unpaywall | unpaywall | 26244088
pdf | mag | mag-corpus | 25596658
pdf | doi | fatcat-ingest | 8267308
pdf | doi | fatcat-changelog | 3869772
pdf | doi | fatcat-ingest-container | 3515873
pdf | pmc | fatcat-ingest-container | 2028825
pdf | arxiv | fatcat-ingest | 630719
pdf | arxiv | fatcat-changelog | 91157
pdf | pmc | fatcat-ingest | 10195
pdf | pmc | fatcat-changelog | 4626
pdf | cnki_covid19 | scrape-covid19 | 2034
pdf | wanfang_covid19 | scrape-covid19 | 975
pdf | spn | savepapernow-web | 103
pdf | arxiv | fatcat-ingest-container | 26
pdf | doi | savepapernow-web | 15
(15 rows)
Uncrawled requests by source:
# TODO: verify this?
SELECT ingest_request.ingest_type, ingest_request.link_source, COUNT(*)
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_request.base_url = ingest_file_result.base_url
AND ingest_request.ingest_type = ingest_file_result.ingest_type
WHERE ingest_file_result.base_url IS NULL
GROUP BY ingest_request.ingest_type, ingest_request.link_source ORDER BY COUNT DESC LIMIT 25;
ingest_type | link_source | count
-------------+-------------+-------
pdf | mag | 47
pdf | unpaywall | 1
(2 rows)
Results by source:
SELECT
ingest_request.ingest_type,
ingest_request.link_source,
COUNT(*) as attempts,
COUNT(CASE WHEN ingest_file_result.hit THEN 1 END) hits,
ROUND(1.0 * COUNT(CASE WHEN ingest_file_result.hit THEN 1 END) / COUNT(*), 3) as fraction
FROM ingest_request
LEFT JOIN ingest_file_result
ON ingest_request.base_url = ingest_file_result.base_url
AND ingest_request.ingest_type = ingest_file_result.ingest_type
AND ingest_file_result.ingest_type IS NOT NULL
GROUP BY ingest_request.ingest_type, ingest_request.link_source ORDER BY attempts DESC LIMIT 25;
ingest_type | link_source | attempts | hits | fraction
-------------+-----------------+----------+----------+----------
pdf | unpaywall | 26244088 | 19968092 | 0.761
pdf | mag | 25596658 | 18712912 | 0.731
pdf | doi | 15653166 | 2878833 | 0.184
pdf | pmc | 2043646 | 1279529 | 0.626
pdf | arxiv | 721902 | 592394 | 0.821
pdf | cnki_covid19 | 2034 | 0 | 0.000
pdf | wanfang_covid19 | 975 | 764 | 0.784
pdf | spn | 103 | 82 | 0.796
Ingest result by status:
SELECT ingest_type, status, COUNT(*) FROM ingest_file_result GROUP BY ingest_type, status ORDER BY COUNT DESC LIMIT 25;
ingest_type | status | count
-------------+-------------------------------------+----------
pdf | success | 37449502
pdf | no-pdf-link | 10908442
pdf | no-capture | 5643670
pdf | redirect-loop | 4823502
pdf | terminal-bad-status | 1715056
pdf | link-loop | 1425072
pdf | cdx-error | 535365
pdf | gateway-timeout | 267654
pdf | skip-url-blocklist | 220433
pdf | wrong-mimetype | 189804
pdf | spn2-cdx-lookup-failure | 103926
pdf | spn-error | 101777
pdf | wayback-error | 93517
pdf | null-body | 87279
pdf | invalid-host-resolution | 35305
pdf | spn-remote-error | 28888
pdf | petabox-error | 12406
pdf | spn2-error | 2905
pdf | spn2-error:job-failed | 2307
pdf | other-mimetype | 2305
pdf | redirects-exceeded | 745
pdf | spn2-error:proxy-error | 438
pdf | spn2-error:invalid-url-syntax | 406
pdf | spn2-error:soft-time-limit-exceeded | 405
pdf | spn2-error:browser-running-error | 274
(25 rows)
Failures by domain:
SELECT ingest_type, domain, status, COUNT((ingest_type, domain, status))
FROM (
SELECT
ingest_file_result.ingest_type as 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
) t1
WHERE t1.domain != ''
AND t1.status != 'success'
GROUP BY ingest_type, domain, status
ORDER BY COUNT DESC
LIMIT 30;
ingest_type | domain | status | count
-------------+---------------------------------------+---------------------+--------
pdf | ssl.fao.org | no-pdf-link | 862277
pdf | www.researchgate.net | redirect-loop | 749094
pdf | www.e-periodica.ch | no-pdf-link | 747370
pdf | ieeexplore.ieee.org | redirect-loop | 707482
pdf | plutof.ut.ee | no-pdf-link | 685341
pdf | www.gbif.org | no-pdf-link | 670905
pdf | dlc.library.columbia.edu | no-pdf-link | 508281
pdf | figshare.com | no-pdf-link | 400501
pdf | onlinelibrary.wiley.com | no-pdf-link | 399187
pdf | watermark.silverchair.com | terminal-bad-status | 357188
pdf | www.die-bonn.de | redirect-loop | 352903
pdf | academic.oup.com | no-pdf-link | 346828
pdf | iopscience.iop.org | terminal-bad-status | 345147
pdf | linkinghub.elsevier.com | no-capture | 328434
pdf | statisticaldatasets.data-planet.com | no-pdf-link | 312206
pdf | cyberleninka.ru | link-loop | 309525
pdf | www.tandfonline.com | no-pdf-link | 309146
pdf | dialnet.unirioja.es | terminal-bad-status | 307572
pdf | doi.pangaea.de | no-pdf-link | 304924
pdf | journals.sagepub.com | no-pdf-link | 285774
pdf | papers.ssrn.com | link-loop | 282415
pdf | dialnet.unirioja.es | redirect-loop | 274476
pdf | ieeexplore.ieee.org | link-loop | 273607
pdf | catalog.paradisec.org.au | redirect-loop | 234653
pdf | www.plate-archive.org | no-pdf-link | 209217
pdf | zenodo.org | no-pdf-link | 200078
pdf | zenodo.org | no-capture | 199025
pdf | spectradspace.lib.imperial.ac.uk:8443 | no-pdf-link | 187084
pdf | digi.ub.uni-heidelberg.de | no-pdf-link | 187039
pdf | validate.perfdrive.com | no-pdf-link | 180191
(30 rows)
Success by domain:
SELECT ingest_type, domain, status, COUNT((ingest_type, domain, status))
FROM (
SELECT
ingest_file_result.ingest_type as 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
) t1
WHERE t1.domain != ''
AND t1.status = 'success'
GROUP BY ingest_type, domain, status
ORDER BY COUNT DESC
LIMIT 30;
ingest_type | domain | status | count
-------------+----------------------------+---------+---------
pdf | www.jstage.jst.go.jp | success | 2244620
pdf | europepmc.org | success | 1284770
pdf | link.springer.com | success | 1017998
pdf | www.scielo.br | success | 799577
pdf | arxiv.org | success | 592622
pdf | downloads.hindawi.com | success | 527278
pdf | res.mdpi.com | success | 501093
pdf | hal.archives-ouvertes.fr | success | 447877
pdf | digital.library.unt.edu | success | 404460
pdf | www.cambridge.org | success | 394666
pdf | dergipark.org.tr | success | 373706
pdf | journals.plos.org | success | 296994
pdf | watermark.silverchair.com | success | 275562
pdf | www.nature.com | success | 263836
pdf | cds.cern.ch | success | 223057
pdf | www.pnas.org | success | 220488
pdf | s3-eu-west-1.amazonaws.com | success | 214558
pdf | www.jbc.org | success | 205277
pdf | www.redalyc.org | success | 193591
pdf | iopscience.iop.org | success | 175796
pdf | apps.dtic.mil | success | 170589
pdf | zenodo.org | success | 167812
pdf | peerj.com | success | 155620
pdf | www.biorxiv.org | success | 149337
pdf | 210.101.116.28 | success | 145706
pdf | www.teses.usp.br | success | 145438
pdf | absimage.aps.org | success | 144400
pdf | hrcak.srce.hr | success | 134669
pdf | www.erudit.org | success | 131771
pdf | babel.hathitrust.org | success | 130645
(30 rows)
## Fatcat Files
Count of PDF files that GROBID processed and matched to a release (via
glutton), but no PDF in `fatcat_file`:
SELECT COUNT(*) as total_count, COUNT(DISTINCT grobid.fatcat_release) as release_count
FROM grobid
LEFT JOIN fatcat_file ON grobid.sha1hex = fatcat_file.sha1hex
WHERE fatcat_file.sha1hex IS NULL
AND grobid.fatcat_release IS NOT NULL;
=> NOT RUN, fatcat_file table is way out of date
|
