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|
Summary:
- very many more PDFs have been grobid-ed vs. pdf_meta-ed
- about 1 million file_meta still have partial metadata (eg, no sha256)
- database size still under 0.5 TByte
- there are about a million CDX error ingest requests, and hundreds of
thousands of SPN errors which could be re-run
## 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 | 42 GB | 84 GB
"public"."ingest_request" | 34 GB | 39 GB | 73 GB
"public"."grobid_shadow" | 64 GB | 6902 MB | 71 GB
"public"."grobid" | 61 GB | 7742 MB | 69 GB
"public"."file_meta" | 32 GB | 29 GB | 61 GB
"public"."ingest_file_result" | 24 GB | 36 GB | 60 GB
"public"."shadow" | 9111 MB | 10204 MB | 19 GB
"public"."fatcat_file" | 12 GB | 6656 MB | 18 GB
"public"."pdf_meta" | 8018 MB | 1966 MB | 9984 MB
"public"."pdftrio" | 618 MB | 432 MB | 1051 MB
"public"."petabox" | 403 MB | 594 MB | 997 MB
(11 rows)
Size: 466.91G
## 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
-------------+-----------------
161944425 | 204,402,677,360,189
(1 row)
# 161.9 mil; 204 TByte
Top mimetypes:
SELECT mimetype, COUNT(*) FROM file_meta GROUP BY mimetype ORDER BY COUNT DESC LIMIT 10;
mimetype | count
-------------------------------+-----------
application/pdf | 161691608
application/octet-stream | 154348
application/xml | 42170
text/html | 18703
text/plain | 15989
application/gzip | 6484
| 6036
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
---------
1015337
(1 row)
## CDX
Total and unique-by-sha1 counts:
SELECT COUNT(DISTINCT sha1hex) as unique_sha1, COUNT(*) as total FROM cdx;
unique_sha1 | total
-------------+-----------
96537611 | 116281981
(1 row)
mimetype counts:
SELECT mimetype, COUNT(*) FROM cdx GROUP BY mimetype ORDER BY COUNT(*) DESC LIMIT 25;
mimetype | count
---------------------------------------------------+-----------
application/pdf | 108706978
warc/revisit | 5912013
text/xml | 519042
application/octet-stream | 307782
text/html | 295634
unk | 156937
application/postscript | 81079
application/save | 80871
binary/octet-stream | 61263
text/plain | 31495
application/x-download | 30511
application/download | 26716
image/pdf | 26357
application/force-download | 10541
multipart/form-data | 5551
application/x-msdownload | 3724
application/x-octetstream | 3216
application | 3171
.pdf | 2728
application/x-pdf | 2563
application/binary | 1306
application/pdf' | 1192
pdf | 1180
[...]
## GROBID
Counts:
SELECT COUNT(*) AS total_files, COUNT(DISTINCT fatcat_release) AS unique_releases FROM grobid;
total_files | unique_releases
-------------+-----------------
95557413 | 18020570
Status?
SELECT status_code, COUNT(*) FROM grobid GROUP BY status_code ORDER BY COUNT DESC LIMIT 10;
status_code | count
-------------+----------
200 | 88450610
500 | 7101098
-4 | 4133
503 | 110
SELECT status, COUNT(*) FROM grobid GROUP BY ORDER BY COUNT DESC LIMIT 10;
status | count
----------------+----------
success | 73814297
| 14638412
error | 7101308
error-timeout | 4133
bad-grobid-xml | 6
(5 rows)
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 | 73813427
| 14638425
## 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 | oai | 51185088
pdf | mag | 35015357
pdf | unpaywall | 27653003
pdf | doi | 16589669
pdf | pmc | 2231113
pdf | arxiv | 794693
pdf | cnki_covid19 | 2034
pdf | wanfang_covid19 | 975
pdf | spn | 148
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 | oai | metha-bulk | 51185088
pdf | mag | mag-corpus | 35015357
pdf | unpaywall | unpaywall | 27653003
pdf | doi | fatcat-ingest | 8320832
pdf | doi | fatcat-changelog | 4752956
pdf | doi | fatcat-ingest-container | 3515873
pdf | pmc | fatcat-ingest-container | 2028825
pdf | arxiv | fatcat-ingest | 630750
pdf | pmc | fatcat-ingest | 194781
pdf | arxiv | fatcat-changelog | 163924
pdf | pmc | fatcat-changelog | 7507
pdf | cnki_covid19 | scrape-covid19 | 2034
pdf | wanfang_covid19 | scrape-covid19 | 975
pdf | spn | savepapernow-web | 148
pdf | arxiv | fatcat-ingest-container | 26
pdf | doi | savepapernow-web | 19
pdf | arxiv | savepapernow-web | 2
Uncrawled requests by source:
# TODO: verify this? seems wrong
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 | 4097008
pdf | oai | 15287
pdf | unpaywall | 1
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 35;
ingest_type | link_source | attempts | hits | fraction
-------------+-----------------+----------+----------+----------
pdf | oai | 51185088 | 5346057 | 0.104
pdf | mag | 35015357 | 22199271 | 0.634
pdf | unpaywall | 27653003 | 22067338 | 0.798
pdf | doi | 16589700 | 3207661 | 0.193
pdf | pmc | 2231113 | 1696976 | 0.761
pdf | arxiv | 794727 | 645607 | 0.812
pdf | cnki_covid19 | 2034 | 0 | 0.000
pdf | wanfang_covid19 | 975 | 764 | 0.784
pdf | spn | 148 | 114 | 0.770
(9 rows)
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 | 46465271
pdf | no-capture | 46115869
pdf | no-pdf-link | 13877460
pdf | redirect-loop | 5943956
pdf | terminal-bad-status | 1962754
pdf | link-loop | 1630078
pdf | cdx-error | 1014409
pdf | gateway-timeout | 459340
pdf | wrong-mimetype | 321774
pdf | skip-url-blocklist | 220629
pdf | wayback-error | 220453
pdf | spn2-cdx-lookup-failure | 143963
pdf | null-body | 113384
pdf | spn-error | 101773
pdf | invalid-host-resolution | 37367
pdf | spn-remote-error | 28886
pdf | petabox-error | 22997
pdf | spn2-error | 16342
pdf | spn2-error:job-failed | 5017
pdf | other-mimetype | 2305
pdf | redirects-exceeded | 746
pdf | spn2-error:soft-time-limit-exceeded | 632
pdf | spn2-error:proxy-error | 437
pdf | spn2-error:invalid-url-syntax | 417
pdf | timeout | 417
(25 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;
total_count | release_count
-------------+---------------
5862666 | 4728824
(1 row)
## PDF Meta
Total rows:
SELECT COUNT(*) as total_count FROM pdf_meta;
total_count
-------------
21961874
By status:
SELECT status, COUNT(*) from pdf_meta GROUP BY status ORDER BY COUNT(*) DESC;
status | count
----------------+----------
success | 21788507
parse-error | 78196
text-too-large | 60595
not-pdf | 31679
error-wayback | 2639
bad-unicode | 251
bad-pdf | 6
empty-blob | 1
(8 rows)
|
