aboutsummaryrefslogtreecommitdiffstats
path: root/sql
diff options
context:
space:
mode:
Diffstat (limited to 'sql')
-rw-r--r--sql/stats/2021-11-26_stats.txt424
-rw-r--r--sql/stats/README.md13
2 files changed, 425 insertions, 12 deletions
diff --git a/sql/stats/2021-11-26_stats.txt b/sql/stats/2021-11-26_stats.txt
new file mode 100644
index 0000000..3a0e561
--- /dev/null
+++ b/sql/stats/2021-11-26_stats.txt
@@ -0,0 +1,424 @@
+
+Date: Sat 27 Nov 2021 03:33:30 AM UTC
+
+## SQL Table Sizes
+
+ Size: 937.28G
+
+ 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"."crossref" | 393 GB | 10127 MB | 403 GB
+ "public"."ingest_request" | 44 GB | 41 GB | 84 GB
+ "public"."cdx" | 52 GB | 28 GB | 80 GB
+ "public"."grobid" | 72 GB | 6963 MB | 79 GB
+ "public"."ingest_file_result" | 38 GB | 40 GB | 78 GB
+ "public"."grobid_shadow" | 67 GB | 5455 MB | 73 GB
+ "public"."file_meta" | 34 GB | 21 GB | 55 GB
+ "public"."pdf_meta" | 20 GB | 5869 MB | 26 GB
+ "public"."grobid_refs" | 19 GB | 1690 MB | 21 GB
+ "public"."fatcat_file" | 12 GB | 6602 MB | 18 GB
+ "public"."shadow" | 9517 MB | 8026 MB | 17 GB
+ "public"."html_meta" | 1200 MB | 8072 kB | 1208 MB
+ "public"."petabox" | 403 MB | 461 MB | 864 MB
+ "public"."pdftrio" | 550 MB | 297 MB | 847 MB
+ "public"."ingest_fileset_platform" | 8192 bytes | 16 kB | 24 kB
+ "public"."crossref_with_refs" | 0 bytes | 0 bytes | 0 bytes
+ (16 rows)
+
+
+## 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
+ -------------+-----------------
+ 179761501 | 244453538203113
+
+ # 179m files, 244 TB
+
+Top mimetypes:
+
+ SELECT mimetype, COUNT(*) FROM file_meta GROUP BY mimetype ORDER BY COUNT DESC LIMIT 30;
+
+ mimetype | count
+ ---------------------------------------------------------------------------+-----------
+ application/pdf | 179376819
+ application/octet-stream | 155379
+ text/html | 116102
+ application/xml | 42170
+ application/xhtml+xml | 24347
+ text/plain | 15990
+ application/jats+xml | 6899
+ application/gzip | 6491
+ | 6034
+ application/postscript | 4912
+ application/vnd.ms-powerpoint | 1672
+ application/msword | 921
+ application/x-bzip2 | 891
+ image/jpeg | 794
+ image/gif | 389
+ application/vnd.openxmlformats-officedocument.wordprocessingml.document | 303
+ application/x-compress | 272
+ application/zip | 131
+ image/png | 121
+ application/CDFV2-unknown | 99
+ application/mac-binhex40 | 79
+ application/vnd.openxmlformats-officedocument.spreadsheetml.sheet | 57
+ application/x-dosexec | 51
+ text/x-tex | 44
+ application/vnd.openxmlformats-officedocument.presentationml.presentation | 39
+ text/x-php | 37
+ text/rtf | 33
+ application/x-dvi | 29
+ application/x-rar | 29
+ video/mp4 | 29
+ (30 rows)
+
+Missing full metadata:
+
+ SELECT COUNT(*) FROM file_meta WHERE sha256hex IS NULL;
+
+ count
+ -------
+ 62196
+
+## CDX
+
+Total and unique-by-sha1 counts:
+
+ SELECT COUNT(DISTINCT sha1hex) as unique_sha1, COUNT(*) as total FROM cdx;
+
+ unique_sha1 | total
+ -------------+-----------
+ 119049962 | 149169240
+
+
+mimetype counts:
+
+ SELECT mimetype, COUNT(*) FROM cdx GROUP BY mimetype ORDER BY COUNT(*) DESC LIMIT 30;
+
+ mimetype | count
+ ----------------------------+-----------
+ application/pdf | 137271670
+ warc/revisit | 9709493
+ application/octet-stream | 590443
+ text/xml | 525481
+ text/html | 421030
+ unk | 207442
+ application/postscript | 81123
+ application/save | 80988
+ binary/octet-stream | 67476
+ image/pdf | 39419
+ application/x-download | 38278
+ text/plain | 36159
+ application/download | 34328
+ application/force-download | 19729
+ multipart/form-data | 9105
+ application | 5299
+ application/x-msdownload | 3851
+ application/x-octetstream | 3649
+ .pdf | 3318
+ application/x-pdf | 2992
+ pdf | 1484
+ file | 1364
+ application/binary | 1354
+ file/unknown | 1345
+ application/pdf' | 1196
+ application/octetstream | 1029
+ application/unknown | 1000
+ 0 | 764
+ text/pdf | 704
+ application/blob | 673
+ (30 rows)
+
+## GROBID
+
+Counts:
+
+ SELECT COUNT(*) AS total_files FROM grobid;
+
+ total_files
+ -------------
+ 111236904
+
+Status?
+
+ SELECT status_code, COUNT(*) FROM grobid GROUP BY status_code ORDER BY COUNT DESC LIMIT 25;
+
+ status_code | count
+ -------------+-----------
+ 200 | 102962304
+ 500 | 8269129
+ -4 | 5013
+ 503 | 548
+
+TODO: how many failed, by mimetype? to check if we are (or have) run non-PDF
+files through by mistake
+
+What version used?
+
+ SELECT grobid_version, COUNT(*) FROM grobid WHERE status_code = 200 GROUP BY grobid_version ORDER BY COUNT DESC LIMIT 25;
+
+ grobid_version | count
+ ----------------------+----------
+ 0.5.5-fatcat | 89983404
+ | 12892161
+ 0.7.0-104-gbeebd9a6b | 86739
+
+## 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 | 43701948
+ pdf | unpaywall | 37802895
+ pdf | doi | 28736398
+ pdf | doaj | 4264610
+ html | doaj | 2429003
+ pdf | pmc | 2383398
+ pdf | arxiv | 2330054
+ html | doi | 39725
+ xml | doaj | 9442
+ pdf | cnki_covid19 | 2034
+ pdf | wanfang_covid19 | 975
+ pdf | spn | 689
+ html | spn | 48
+ xml | spn | 1
+ (15 rows)
+
+ 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 35;
+
+ ingest_type | link_source | ingest_request_source | count
+ -------------+-----------------+-------------------------+----------
+ pdf | oai | metha-bulk | 51185088
+ pdf | mag | mag-corpus | 43701948
+ pdf | unpaywall | unpaywall | 37802895
+ pdf | doi | fatcat-changelog | 16207728
+ pdf | doi | fatcat-ingest | 9012282
+ pdf | doaj | doaj | 4264610
+ pdf | doi | fatcat-ingest-container | 3515873
+ html | doaj | doaj | 2429003
+ pdf | pmc | fatcat-ingest-container | 2028825
+ pdf | arxiv | fatcat-ingest | 1767705
+ pdf | arxiv | fatcat-changelog | 562320
+ pdf | pmc | fatcat-ingest | 297527
+ pdf | pmc | fatcat-changelog | 57046
+ html | doi | fatcat-ingest | 37788
+ xml | doaj | doaj | 9442
+ pdf | cnki_covid19 | scrape-covid19 | 2034
+ html | doi | fatcat-changelog | 1897
+ pdf | wanfang_covid19 | scrape-covid19 | 975
+ pdf | spn | savepapernow-web | 689
+ pdf | doi | savepapernow-web | 613
+ html | spn | savepapernow-web | 48
+ html | doi | savepapernow-web | 40
+ pdf | arxiv | fatcat-ingest-container | 26
+ pdf | arxiv | savepapernow-web | 3
+ xml | spn | savepapernow-web | 1
+ (25 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 35;
+
+ ingest_type | link_source | count
+ -------------+-------------+--------
+ pdf | mag | 169076
+ pdf | oai | 15283
+ pdf | doaj | 2063
+ html | doaj | 620
+ pdf | doi | 22
+ pdf | unpaywall | 17
+
+
+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 | 14554221 | 0.284
+ pdf | mag | 43701948 | 32643175 | 0.747
+ pdf | unpaywall | 37802895 | 29989257 | 0.793
+ pdf | doi | 28736547 | 7690393 | 0.268
+ pdf | doaj | 4264610 | 2851601 | 0.669
+ html | doaj | 2429003 | 122937 | 0.051
+ pdf | pmc | 2383398 | 1821071 | 0.764
+ pdf | arxiv | 2330054 | 2159738 | 0.927
+ html | doi | 39725 | 1235 | 0.031
+ xml | doaj | 9442 | 6897 | 0.730
+ pdf | cnki_covid19 | 2034 | 0 | 0.000
+ pdf | wanfang_covid19 | 975 | 764 | 0.784
+ pdf | spn | 689 | 503 | 0.730
+ html | spn | 48 | 5 | 0.104
+ xml | spn | 1 | 0 | 0.000
+
+Ingest result by status:
+
+ SELECT ingest_type, status, COUNT(*) FROM ingest_file_result GROUP BY ingest_type, status ORDER BY COUNT DESC LIMIT 50;
+
+
+ ingest_type | status | count
+ -------------+-------------------------------+----------
+ pdf | success | 78944243
+ pdf | no-pdf-link | 26270027
+ pdf | no-capture | 23267156
+ pdf | redirect-loop | 9837466
+ pdf | terminal-bad-status | 4147454
+ pdf | skip-url-blocklist | 3088907
+ pdf | link-loop | 2953891
+ pdf | blocked-cookie | 1855541
+ html | wrong-scope | 1106171
+ pdf | wrong-mimetype | 859941
+ pdf | gateway-timeout | 729771
+ pdf | spn2-cdx-lookup-failure | 584856
+ html | no-capture | 423917
+ pdf | forbidden | 390804
+ pdf | cdx-error | 363091
+ pdf | wayback-content-error | 354894
+ pdf | null-body | 341698
+ pdf | too-many-redirects | 307096
+ pdf | not-found | 294592
+ html | redirect-loop | 213032
+ html | unknown-scope | 207923
+ pdf | spn2-error | 192046
+ html | html-resource-no-capture | 166119
+ html | success | 124177
+ pdf | wayback-error | 105385
+ html | null-body | 100296
+ pdf | spn2-wayback-error | 73176
+ pdf | remote-server-error | 60908
+ pdf | spn2-error:too-many-redirects | 58076
+ pdf | skip-wall | 57744
+ html | wayback-content-error | 53928
+ pdf | read-timeout | 42465
+ pdf | invalid-host-resolution | 37221
+ pdf | petabox-error | 28765
+ pdf | spn2-error:unknown | 23885
+ html | wrong-mimetype | 18930
+ pdf | bad-redirect | 14708
+ html | terminal-bad-status | 14070
+ html | petabox-error | 13770
+ html | spn2-cdx-lookup-failure | 13002
+ pdf | spn2-error:job-failed | 9721
+ html | cdx-error | 7167
+ xml | success | 6897
+ pdf | spn2-error:bad-request | 4433
+ pdf | spn-remote-error | 4206
+ pdf | body-too-large | 3019
+ xml | null-body | 2353
+ pdf | other-mimetype | 2304
+ pdf | error | 1900
+ pdf | spn2-error:proxy-error | 1850
+ (50 rows)
+
+Failed ingest by terminal status code:
+
+ SELECT ingest_type, terminal_status_code, COUNT(*) FROM ingest_file_result WHERE hit = false GROUP BY ingest_type, terminal_status_code ORDER BY COUNT DESC LIMIT 50;
+
+ ingest_type | terminal_status_code | count
+ -------------+----------------------+----------
+ pdf | 200 | 36821458
+ pdf | | 26058729
+ pdf | 301 | 8466302
+ html | 200 | 1676730
+ pdf | 503 | 1028504
+ pdf | 302 | 949465
+ pdf | 403 | 936737
+ pdf | 404 | 687661
+ pdf | 400 | 507303
+ html | | 439356
+ pdf | 401 | 288994
+ pdf | 500 | 263775
+ html | 301 | 211796
+ pdf | 303 | 130719
+ pdf | 410 | 66495
+ pdf | 502 | 41760
+ pdf | 429 | 35266
+ pdf | 420 | 26722
+ pdf | 409 | 15204
+ pdf | 509 | 15113
+ pdf | 999 | 11409
+ html | 404 | 9578
+ pdf | 307 | 8404
+ pdf | 308 | 5514
+ pdf | 202 | 4724
+ html | 500 | 3628
+ xml | 200 | 2537
+ pdf | 520 | 2199
+ pdf | 206 | 1694
+ html | 302 | 1138
+ pdf | 504 | 1124
+ pdf | 521 | 1085
+ pdf | 412 | 921
+ pdf | 421 | 714
+ pdf | 300 | 461
+ pdf | 505 | 436
+ pdf | 406 | 427
+ pdf | 508 | 408
+ html | 403 | 382
+ html | 503 | 378
+ html | 303 | 268
+ pdf | 204 | 252
+ pdf | 226 | 166
+ pdf | 402 | 70
+ html | 502 | 68
+ pdf | 523 | 55
+ pdf | 408 | 53
+ pdf | 432 | 45
+ pdf | 530 | 31
+ pdf | 416 | 31
+ (50 rows)
diff --git a/sql/stats/README.md b/sql/stats/README.md
index 62e213c..3161514 100644
--- a/sql/stats/README.md
+++ b/sql/stats/README.md
@@ -49,7 +49,7 @@ mimetype counts:
Counts:
- SELECT COUNT(*) AS total_files, COUNT(DISTINCT fatcat_release) AS unique_releases FROM grobid;
+ SELECT COUNT(*) AS total_files FROM grobid;
Status?
@@ -107,14 +107,3 @@ Failed ingest by terminal status code:
SELECT ingest_type, terminal_status_code, COUNT(*) FROM ingest_file_result WHERE hit = false GROUP BY ingest_type, terminal_status_code ORDER BY COUNT DESC LIMIT 50;
-## 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;
-
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-21 18:00:05 +0000