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| author | Martin Czygan <martin.czygan@gmail.com> | 2021-09-28 13:39:28 +0200 |
|---|---|---|
| committer | Martin Czygan <martin.czygan@gmail.com> | 2021-09-28 13:39:28 +0200 |
| commit | 6d748f3c24cf5fd21316a2182a368342d0bf1427 (patch) | |
| tree | 35efdf359950a018ee48f8b0549cd9340337ef04 /python | |
| parent | 4d109a3fd5940ef27ed3e68fdebf0ccd3f234c28 (diff) | |
| download | refcat-6d748f3c24cf5fd21316a2182a368342d0bf1427.tar.gz refcat-6d748f3c24cf5fd21316a2182a368342d0bf1427.zip | |
mag: notes on doi-to-doi refs
Diffstat (limited to 'python')
| -rw-r--r-- | python/refcat/report.py | 22 |
1 files changed, 21 insertions, 1 deletions
diff --git a/python/refcat/report.py b/python/refcat/report.py index ae4844d..4a0c219 100644 --- a/python/refcat/report.py +++ b/python/refcat/report.py @@ -77,7 +77,7 @@ class BrefDOIOnly(Refcat): # $ unpigz -c /magna/data/mag-2021-06-07/Papers.txt.gz | cut -f1,3 | awk '$2 != ""' | pv -l > /dev/null # 96.7M 0:11:05 [ 145k/s] # -# time unpigz -c /magna/data/mag-2021-06-07/Papers.txt.gz | cut -f1,3 | awk '$2 != ""' | mkocidb -o mag_id_doi.db +# $ time unpigz -c /magna/data/mag-2021-06-07/Papers.txt.gz | cut -f1,3 | awk '$2 != ""' | mkocidb -o mag_id_doi.db # # 2021/09/27 17:08:45 [ok] initialized database -- /sandcrawler-db/tmp-refcat/mag_id_doi.db # written 2.9G -- 3.4M/s @@ -89,4 +89,24 @@ class BrefDOIOnly(Refcat): # real 23m7.744s # user 30m55.642s # sys 4m17.959s +# +# Can use a in memory map, too - sqlite3 lookups for 2B+ items takes a while at +# 30 Kqps; takes 30% of RAM on 48GB, sigh; just map[int]string from paper id to doi. +# +# Prepare the 2-TSV list. +# +# $ time unpigz -c /magna/data/mag-2021-06-07/Papers.txt.gz | cut -f1,3 | awk '$2 != ""' | pv -l > /magna/data/mag-2021-06-07/mapping.tsv +# +# real 15m27.348s +# user 21m4.297s +# sys 3m34.441s +# +# $ time zstdcat -T0 PaperReferences.txt.zst | +# magrefs-mem -f /magna/data/mag-2021-06-07/mapping.tsv | +# pv -l | zstd -c -T0 > doi_refs.tsv.zst +# +# $ zstdcat -T0 doi_refs.tsv.zst| pv -l | wc -l +# 1.32G 0:06:33 [3.34M/s] [ <=> ]1315040677 +# 1315040677 + |