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diff --git a/notes/2021-12_sim_update.md b/notes/2021-12_sim_update.md new file mode 100644 index 0000000..691c916 --- /dev/null +++ b/notes/2021-12_sim_update.md @@ -0,0 +1,319 @@ + +SIM digitization is mostly complete, looking at starting to (re)index. + +Around 2021-12-01, re-ran build of issue DB, with filters like +`(pub_type:"Scholarly Journals" OR pub_type:"Historical Journals" OR +pub_type:"Law Journals")`: + + ia search 'collection:periodicals collection:sim_microfilm mediatype:collection (pub_type:"Scholarly Journals" OR pub_type:"Historical Journals" OR pub_type:"Law Journals")' -n + # 7947 + + ia search 'collection:periodicals collection:sim_microfilm mediatype:texts !noindex:true (pub_type:"Scholarly Journals" OR pub_type:"Historical Journals" OR pub_type:"Law Journals")' -n + # 849593 + +If filters are relaxed, and all microfilm included, could be: + + ia search 'collection:periodicals collection:sim_microfilm mediatype:collection' -n + # 13590 + + ia search 'collection:periodicals collection:sim_microfilm mediatype:texts' -n + # 1870482 + + ia search 'collection:periodicals collection:sim_microfilm mediatype:texts (pub_type:"Scholarly Journals" OR pub_type:"Historical Journals" OR pub_type:"Law Journals")' -n + # 849599 + +With the tighter filters (initially), looking at: + + select count(*) from sim_pub; + 7902 + + select count(*) from sim_pub where container_ident is not null; + 5973 + + select count(*) from sim_pub where issn is not null; + 6107 + + select pub_type, count(*) from sim_pub where issn is null group by pub_type; + pub_type count(*) + Historical Journals 1568 + Law Journals 11 + Scholarly Journals 216 + + select count(*) from sim_issue; + 667073 + + select count(*) from sim_issue where release_count is null; + 373921 + + select count(*) from sim_issue where release_count = 0; + 262125 + + select sum(release_count) from sim_issue; + 534609 + + select sum(release_count) from release_counts; + # PREVIOUSLY: 397,602 + # 8,231,201 + +What container types do we have in fatcat? + + zcat container_export.json.gz | rg "sim_pubid" | jq .extra.ia.sim.pub_type | sort | uniq -c | sort -nr + 7135 "Scholarly Journals" + 2572 "Trade Journals" + 1325 "Magazines" + 187 "Law Journals" + 171 "Government Documents" + 21 "Historical Journals" + +How many releases are we expecting to match? + + fatcat-cli search containers any_ia_sim:true --count + # 11965 + + fatcat-cli search release in_ia_sim:true --count + # 22,470,053 + + fatcat-cli search release in_ia_sim:true container_id:* --count + # 22,470,053 (100%) + + fatcat-cli search release in_ia_sim:true container_id:* year:* --count + # 22,470,053 + + fatcat-cli search release in_ia_sim:true container_id:* volume:* --count + # 20,498,018 + + fatcat-cli search release in_ia_sim:true container_id:* year:* volume:* --count + # 20,498,018 + + fatcat-cli search release in_ia_sim:true container_id:* volume:* issue:* --count + # 7,311,684 + + fatcat-cli search release in_ia_sim:true container_id:* volume:* issue:* pages:* --count + # 7,112,117 + + fatcat-cli search release in_ia_sim:true container_id:* volume:* pages:* --count + # 20,017,423 + + fatcat-cli search release 'in_ia_sim:true container_id:* !issue:*' --count + # 14,737,140 + + fatcat-cli search release 'in_ia_sim:true container_id:* !issue:* doi:* doi_registrar:crossref' --count + # 14,620,485 + + fatcat-cli search release 'in_ia_sim:true container_id:* !issue:* doi:* doi_registrar:crossref in_ia:false' --count + # 12,320,127 + + fatcat-cli search scholar doc_type:work access_type:ia_sim --count + # 66162 + + fatcat-cli search scholar doc_type:sim_page --count + # 10,448,586 + +The large majority of releases which *might* get included, are not. Missing an +issue number is the single largest category; almost all are Crossref DOIs; the +large majority are not in IA otherwise. + +One conclusion from this is that updating fatcat with additional +volume/issue/page metadata (if available) could be valuable. Or, in the +short-term, copying this information from crossref metadata in the +fatcat-scholar pipeline would make sense. + +There is still an open question of why so few of the ~7 million fatcat releases +which *should* match to SIM, are failing to. Is it because they have not been +processed? Or the issues are getting filtered? + +---- + +Queries against chocula DB, to gauge possible breakdown by SIM `pub_type`: + + SELECT * FROM directory + WHERE + slug = 'sim' + AND extra LIKE '%"Scholarly Journals"%' + LIMIT 5; + + SELECT journal.issnl, journal.release_count + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Scholarly Journals"%' + AND journal.issnl IS NOT NULL + LIMIT 5; + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND journal.issnl IS NOT NULL; + # 40,579,513 + + SELECT SUM(journal.release_count - journal.preserved_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND journal.issnl IS NOT NULL; + # 2,692,023 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Scholarly Journals"%' + AND journal.issnl IS NOT NULL; + # 39,020,833 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Trade Journals"%' + AND journal.issnl IS NOT NULL; + # 755,367 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Magazines"%' + AND journal.issnl IS NOT NULL; + # 487,197 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Law Journals"%' + AND journal.issnl IS NOT NULL; + # 78,519 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Government Documents"%' + AND journal.issnl IS NOT NULL; + # 30,786 + + SELECT SUM(journal.release_count) + FROM directory + LEFT JOIN journal ON journal.issnl = directory.issnl + WHERE + slug = 'sim' + AND extra LIKE '%"Historical Journals"%' + AND journal.issnl IS NOT NULL; + # 206,811 + +To summarize counts, remembering that these apply to entire runs of journals +with any coverage in the SIM collection (not by year/volume/issue matching): + + Scholarly: 39,020,833 + Trade: 755,367 + Magazines: 487,197 + Law: 78,519 + Government: 30,786 + Historical: 206,811 + Total: 40,579,513 + "Unpreserved": 2,692,023 + +The TL;DR is that almost everything is "Scholarly Journals", with very little +"Law" or "Historical" coverage. + +---- + +Experimented with a handful of examples, and it seems like newer-processed +(tesseract) SIM does work with the existing pipeline (eg, the djvu files still +work). + +---- + +How many pages exist now, and how many do we expect to index? + + SELECT SUM(last_page-first_page) FROM sim_issue; + # 83,504,593 + + SELECT SUM(last_page-first_page) FROM sim_issue WHERE (release_count IS NULL OR release_count < 5); + SELECT SUM(last_page-first_page) FROM sim_issue WHERE (release_count IS NULL OR release_count < 5); + # 75,907,903 + + fatcat-cli search scholar doc_type:sim_page --count + # 10,448,586 + +Large increase, but not too wild. + +Generate issues metadata: + + # in pipenv shell + python -m fatcat_scholar.sim_pipeline run_print_issues \ + | shuf \ + | parallel -j16 --colsep "\t" python -m fatcat_scholar.sim_pipeline run_fetch_issue {1} {2} \ + | pv -l \ + | pigz \ + > /kubwa/scholar/2021-12-01/sim_intermediate.2021-12-01.json.gz + # 20.2M 13:44:18 [ 408 /s] + +If this runs at 300 pages/sec (aggregate), it will take 3-4 days to extract all +pages. + +Huh, got only a fraction of what was expected. Lots of errors on individual +issues, but that should be fine/expected. + +Let's try a sub-sample of 1000 issues, after also adding some print statements: + + python -m fatcat_scholar.sim_pipeline run_print_issues \ + | shuf -n1000 \ + | parallel -j16 --colsep "\t" python -m fatcat_scholar.sim_pipeline run_fetch_issue {1} {2} \ + | pv -l \ + | pigz \ + > /kubwa/scholar/2021-12-01/sim_intermediate.2021-12-01.1k_issues.json.gz + # 76.1k 0:03:34 [ 354 /s] + + # issue without leaf numbers: sim_journal-of-organizational-and-end-user-computing_1989-1992_1-4_cumulative-index + # issue without leaf numbers: sim_review-of-english-studies_1965_16_contents_0 + +How many issues are attempted? + + python -m fatcat_scholar.sim_pipeline run_print_issues \ + | wc -l + # 268,707 + + SELECT COUNT(*) FROM sim_issue LEFT JOIN sim_pub ON sim_issue.sim_pubid = sim_pub.sim_pubid WHERE sim_issue.release_count < 5; + # 268,707 + + SELECT COUNT(*) FROM sim_issue LEFT JOIN sim_pub ON sim_issue.sim_pubid = sim_pub.sim_pubid WHERE sim_issue.release_count < 5 OR sim_issue.release_count IS NULL; + # 642,015 + + SELECT COUNT(*) FROM sim_issue LEFT JOIN sim_pub ON sim_issue.sim_pubid = sim_pub.sim_pubid WHERE sim_issue.release_count < 100 OR sim_issue.release_count IS NULL; + # 667,023 + +Not including the `OR sim_issue.release_count IS NULL` was a bug. + +Also, should skip additional suffixes: +- _contents_0 +- _cumulative-index +- _index-contents + +With those changes: + + python -m fatcat_scholar.sim_pipeline run_print_issues \ + | wc -l + # 627,304 + +Ok, start the dump again: + + mv /kubwa/scholar/2021-12-01/sim_intermediate.2021-12-01.json.gz /kubwa/scholar/2021-12-01/sim_intermediate.2021-12-01.partial.json.gz + + python -m fatcat_scholar.sim_pipeline run_print_issues \ + | shuf \ + | parallel -j16 --colsep "\t" python -m fatcat_scholar.sim_pipeline run_fetch_issue {1} {2} \ + | pv -l \ + | pigz \ + > /kubwa/scholar/2021-12-01/sim_intermediate.2021-12-01.json.gz + |