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Relevant github issue: https://github.com/internetarchive/fatcat/issues/83
How many existing fatcat releases have a non-lowercase DOI? As of June 2021:
zcat release_extid.tsv.gz | cut -f3 | rg '[A-Z]' | pv -l | wc -l
139964
## Prep
wget https://archive.org/download/fatcat_bulk_exports_2021-11-05/release_extid.tsv.gz
# scratch:bin/fcid.py is roughly the same as `fatcat_util.py uuid2fcid`
zcat release_extid.tsv.gz \
| cut -f1,3 \
| rg '[A-Z]' \
| /fast/scratch/bin/fcid.py \
| pv -l \
> nonlowercase_doi_releases.tsv
# 140k 0:03:54 [ 599 /s]
wc -l nonlowercase_doi_releases.tsv
140530 nonlowercase_doi_releases.tsv
Uhoh, there are ~500 more than previously? Guess those are from after the fix?
Create a sample for testing:
shuf -n10000 nonlowercase_doi_releases.tsv \
> nonlowercase_doi_releases.10k_sample.tsv
## Test in QA
In pipenv:
export FATCAT_AUTH_WORKER_CLEANUP=[...]
head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
| python -m fatcat_tools.cleanups.release_lowercase_doi -
# Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0})
head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
| python -m fatcat_tools.cleanups.release_lowercase_doi -
# Counter({'total': 100, 'skip-existing-doi-fine': 100, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0})
head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
| python -m fatcat_tools.cleanups.release_lowercase_doi -
# no such release_ident found: dcjsybvqanffhmu4dhzdnptave
Presumably because this is being run in QA, and there are some newer prod releases in the snapshot.
Did a quick update, and then:
head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
| python -m fatcat_tools.cleanups.release_lowercase_doi -
# Counter({'total': 2000, 'skip-existing-doi-fine': 1100, 'update': 898, 'skip-existing-not-found': 2, 'skip': 0, 'insert': 0, 'exists': 0})
Did some spot checking in QA. Out of 20 DOIs checked, 15 were valid, 5 were not
valid (doi.org 404). It seems like roughly 1/3 have a dupe DOI (the lower-case
DOI exists); didn't count exact numbers.
This cleanup is simple and looks good to go. Batch size of 50 is good for full
releases.
Example of parallelization:
cat /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
| parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.release_lowercase_doi -
Ready to go!
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