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diff --git a/extra/bulk_edits/2020-12-14_doaj.md b/extra/bulk_edits/2020-12-14_doaj.md new file mode 100644 index 00000000..5e897183 --- /dev/null +++ b/extra/bulk_edits/2020-12-14_doaj.md @@ -0,0 +1,139 @@ + +## Earlier QA Testing (November 2020) + + export FATCAT_API_AUTH_TOKEN=... (FATCAT_AUTH_WORKER_DOAJ) + + # small test: + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | head | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + # full run + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | pv -l | parallel -j12 --round-robin --pipe ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + before: 519.17G + after: 542.08G + + + 5.45M 6:29:17 [ 233 /s] + + 12x of: + Counter({'total': 455504, 'insert': 394437, 'exists': 60615, 'skip': 452, 'skip-title': 452, 'update': 0}) + + total: ~5,466,048 + insert: ~4,733,244 + exists: ~727,380 + +Initial imports (before crash) were like: + + Counter({'total': 9339, 'insert': 9330, 'skip': 9, 'skip-title': 9, 'update': 0, 'exists': 0}) + +Seems like there is a bug, not finding existing by DOI? + +## Prod Container Metadata Update (chocula) + +Generic update of container metadata using chocula pipeline. Need to run this +before DOAJ import to ensure we have all the containers already updated. + +Also updating ISSN-L index at the same time. Using a 2020-11-19 metadata +snapshot, which was generated on 2020-12-07; more recent snapshots had small +upstream changes in some formats so it wasn't trivial to run with a newer +snapshot. + + # git rev: 9f67c82ce8952bbe9a7a07b732830363c7865485 + + # from laptop, then unzip on prod machine + scp chocula_fatcat_export.2020-11-19.json.gz fatcat-prod1-vm:/srv/fatcat/datasets/ + + # check ISSN-L symlink + # ISSN-to-ISSN-L.txt -> 20201119.ISSN-to-ISSN-L.txt + + export FATCAT_AUTH_WORKER_JOURNAL_METADATA=... + head -n200 /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json | ./fatcat_import.py chocula - + Counter({'total': 200, 'exists': 200, 'exists-by-issnl': 6, 'skip': 0, 'insert': 0, 'update': 0}) + + head -n200 /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json | ./fatcat_import.py chocula - --do-updates + Counter({'total': 200, 'exists': 157, 'exists-skip-update': 151, 'update': 43, 'exists-by-issnl': 6, 'skip': 0, 'insert': 0}) + +Some of these are very minor updates, so going to do just creation (no +`--do-updates`) to start. + + time ./fatcat_import.py chocula /srv/fatcat/datasets/chocula_fatcat_export.2020-11-19.json + Counter({'total': 168165, 'exists': 167497, 'exists-by-issnl': 2371, 'insert': 668, 'skip': 0, 'update': 0}) + + real 5m37.081s + user 3m1.648s + sys 0m9.488s + +TODO: tweak chocula import script to not update on `extra.state` metadata. + + +## Release Metadata Bulk Import + +This is the first production bulk import of DOAJ metadata! + + # git rev: 9f67c82ce8952bbe9a7a07b732830363c7865485 + # DB before: Size: 678.15G + + # ensure fatcatd is updated to have support for DOAJ identifier + + # create new bot user + ./target/release/fatcat-auth create-editor --admin --bot doaj-bot + => mir5imb3v5ctxcaqnbstvmri2a + + ./target/release/fatcat-auth create-token mir5imb3v5ctxcaqnbstvmri2a + => ... + + # download dataset + wget https://archive.org/download/doaj_data_2020-11-13/doaj_article_data_2020-11-13.sample_10k.json.gz + wget https://archive.org/download/doaj_data_2020-11-13/doaj_article_data_2020-11-13_all.json.gz + + export FATCAT_AUTH_WORKER_DOAJ=... + + # start small + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13.sample_10k.json.gz | head -n100 | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 100, 'exists': 70, 'insert': 30, 'skip': 0, 'update': 0}) + +That is about expected, in terms of fraction without DOI. However, 6 out of 10 +(randomly checked) of the inserted releases seem to be dupes, which feels too +high. So going to pause this import until basic fuzzy matching ready from +Martin's fuzzycat work, and will check against elasticsearch before import. +Will shuffle the entire file, import in a single thread, and just skip +importing if there is any fuzzy match (not try to merge/update). Expecting +about 500k new releases after such filtering. + +Ok, on 2020-12-17, back with patches to use fuzzycat in filtering. Trying +another batch: + + # git rev: 60e022609cd3fbbf9634577149018592e680858d + # DB before: Size: 678.47G + + export FATCAT_AUTH_WORKER_DOAJ=... + + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13.sample_10k.json.gz | head -n1000 | tail -n100 | ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + => Counter({'total': 100, 'exists': 71, 'insert': 19, 'exists-fuzzy': 10, 'skip': 0, 'update': 0}) + + # https://fatcat.wiki/changelog/5033496 + +Sampled 10x of these and they look much better: no obvious duplication. Going +ahead with the full import; note that other ingest is happening in parallel +(many crossref, datacite, and pubmed imports which backed up). + + # full run + # note the shuf command added, in an attempt to reduce duplicates within this corpus + zcat /srv/fatcat/datasets/doaj_article_data_2020-11-13_all.json.gz | shuf | pv -l | parallel -j12 --round-robin --pipe ./fatcat_import.py doaj-article --issn-map-file /srv/fatcat/datasets/ISSN-to-ISSN-L.txt - + + # started 2020-12-17 22:01 (Pacific) + + => 5.45M 52:38:45 [28.8 /s] + => Counter({'total': 1366458, 'exists': 1020295, 'insert': 200249, 'exists-fuzzy': 144334, 'skip': 1563, 'skip-title': 1563, 'skip-doaj-id-mismatch': 17, 'update': 0}) + +As total estimates: + +- total: 5,465,832 +- exists: 4,081,180 +- exists-fuzzy: 577,336 +- insert: 800,996 + +Ending database size: Size: 684.08G + +(note that regular imports were running during same period) + |