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Diffstat (limited to 'python/README_import.md')
| -rw-r--r-- | python/README_import.md | 104 |
1 files changed, 24 insertions, 80 deletions
diff --git a/python/README_import.md b/python/README_import.md index d481b7ae..5f5a845e 100644 --- a/python/README_import.md +++ b/python/README_import.md @@ -8,6 +8,14 @@ Run in order: Lots of trouble with encoding; always `export LC_ALL=C.UTF-8` +Start off with: + + sudo su webcrawl + cd /srv/fatcat/src/python + export LC_ALL=C.UTF-8 + pipenv shell + export LC_ALL=C.UTF-8 + ## Data Sources Download the following; uncompress the sqlite file, but **do not** uncompress @@ -18,102 +26,38 @@ the others: https://archive.org/download/ia_journal_metadata_explore_2018-04-05/journal_extra_metadata.csv https://archive.org/download/issn_issnl_mappings/20180216.ISSN-to-ISSN-L.txt https://archive.org/download/orcid-dump-2017/public_profiles_API-2.0_2017_10_json.tar.gz + https://archive.org/download/ia_journal_pid_map_munge_20180908/release_ids.ia_munge_20180908.sqlite3.gz + https://archive.org/download/ia_test_paper_matches/2018-08-27-2352.17-matchcrossref.insertable.json.gz + https://archive.org/download/ia_papers_manifest_2018-01-25_matched/ia_papers_manifest_2018-01-25.matched.json.gz ## ISSN From CSV file: - export LC_ALL=C.UTF-8 - time ./fatcat_import.py import-issn /srv/datasets/journal_extra_metadata.csv - - real 2m42.148s - user 0m11.148s - sys 0m0.336s + # See "start off with" command above + time ./fatcat_import.py import-issn /srv/fatcat/datasets/journal_extra_metadata.csv -Pretty quick, a few minutes. +Usually a couple minutes at most on fast production machine. ## ORCID -Directly from compressed tarball; takes about 2 hours in production: - - tar xf /srv/datasets/public_profiles_API-2.0_2017_10_json.tar.gz -O | jq -c . | grep '"person":' | time parallel -j12 --pipe --round-robin ./fatcat_import.py import-orcid - - -After tuning database, `jq` CPU seems to be bottleneck, so, from pre-extracted -tarball: - - tar xf /srv/datasets/public_profiles_API-2.0_2017_10_json.tar.gz -O | jq -c . | rg '"person":' > /srv/datasets/public_profiles_1_2_json.all.json - time parallel --bar --pipepart -j8 -a /srv/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid - - -Does not work: - - ./fatcat_import.py import-orcid /data/orcid/partial/public_profiles_API-2.0_2017_10_json/3/0000-0001-5115-8623.json - -Instead: - - cat /data/orcid/partial/public_profiles_API-2.0_2017_10_json/3/0000-0001-5115-8623.json | jq -c . | ./fatcat_import.py import-orcid - - -Or for many files: - - find /data/orcid/partial/public_profiles_API-2.0_2017_10_json/3 -iname '*.json' | parallel --bar jq -c . {} | rg '"person":' | ./fatcat_import.py import-orcid - - -### ORCID Performance +Usually tens of minutes on fast production machine. -for ~9k files: - - (python-B2RYrks8) bnewbold@orithena$ time parallel --pipepart -j4 -a /data/orcid/partial/public_profiles_API-2.0_2017_10_json/all.json ./fatcat_import.py import-orcid - - real 0m15.294s - user 0m28.112s - sys 0m2.408s - - => 636/second - - (python-B2RYrks8) bnewbold@orithena$ time ./fatcat_import.py import-orcid /data/orcid/partial/public_profiles_API-2.0_2017_10_json/all.json - real 0m47.268s - user 0m2.616s - sys 0m0.104s - - => 203/second - -For the full batch, on production machine with 12 threads, around 3.8 million records: - - 3550.76 user - 190.16 system - 1:40:01 elapsed - - => 644/second - -After some simple database tuning: - - 2177.86 user - 145.60 system - 56:41.26 elapsed - - => 1117/second + time parallel --bar --pipepart -j8 -a /srv/fatcat/datasets/public_profiles_1_2_json.all.json ./fatcat_import.py import-orcid - ## Crossref -From compressed: - - xzcat /srv/datasets/crossref-works.2018-01-21.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py import-crossref - /srv/datasets/20180216.ISSN-to-ISSN-L.txt - -## Manifest +Usually 24 hours or so on fast production machine. - time ./fatcat_import.py import-manifest /srv/datasets/idents_files_urls.sqlite + time xzcat /srv/fatcat/datasets/crossref-works.2018-01-21.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py import-crossref - /srv/fatcat/datasets/20180216.ISSN-to-ISSN-L.txt /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3 - [...] - Finished a batch; row 284518671 of 9669646 (2942.39%). Total inserted: 6606900 - Finished a batch; row 284518771 of 9669646 (2942.39%). Total inserted: 6606950 - Finished a batch; row 284518845 of 9669646 (2942.39%). Total inserted: 6607000 - Finished a batch; row 284518923 of 9669646 (2942.39%). Total inserted: 6607050 - Done! Inserted 6607075 - - real 1590m36.626s - user 339m40.928s - sys 19m3.576s +## Matched -Really sped up once not contending with Crossref import, so don't run these two at the same time. +Unknown speed! -## Matched + # No file update for the first import... + zcat /srv/fatcat/datasets/ia_papers_manifest_2018-01-25.matched.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched --no-file-update - - zcat /srv/datasets/2018-08-27-2352.17-matchcrossref.insertable.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched - + # ... but do on the second + zcat /srv/fatcat/datasets/2018-08-27-2352.17-matchcrossref.insertable.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py import-matched - |