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authorBryan Newbold <bnewbold@robocracy.org>2019-05-23 10:52:46 -0700
committerBryan Newbold <bnewbold@robocracy.org>2019-05-23 10:52:46 -0700
commitbbc4ff2e2dbaf024251fe642cd1cca91f921f5b6 (patch)
tree83ad786b317388aa4fe23c9c252ffdb4be712a81
parent124c99a7e02023606d279e766b403ff42734024e (diff)
downloadfatcat-bbc4ff2e2dbaf024251fe642cd1cca91f921f5b6.tar.gz
fatcat-bbc4ff2e2dbaf024251fe642cd1cca91f921f5b6.zip
updated import instructions
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@@ -54,6 +54,48 @@ Usually 24 hours or so on fast production machine.
time xzcat /srv/fatcat/datasets/crossref-works.2018-09-05.json.xz | time parallel -j20 --round-robin --pipe ./fatcat_import.py crossref - /srv/fatcat/datasets/20180216.ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3
+## JALC
+
+First import a random subset single threaded to create (most) containers. On a
+fast machine, this takes a couple minutes.
+
+ time ./fatcat_import.py jalc /srv/fatcat/datasets/JALC-LOD-20180907.sample10k.rdf /srv/fatcat/datasets/ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3
+
+Then, in parallel:
+
+ zcat /srv/fatcat/datasets/JALC-LOD-20180907.gz | pv -l | time parallel -j20 --round-robin --pipe ./fatcat_import.py jalc - /srv/fatcat/datasets/ISSN-to-ISSN-L.txt --extid-map-file /srv/fatcat/datasets/release_ids.ia_munge_20180908.sqlite3
+
+## JSTOR
+
+Looks like:
+
+ fd . /data/jstor/metadata/ | time parallel -j20 --round-robin --pipe ./fatcat_import.py jstor - /data/issn/20190129.ISSN-to-ISSN-L.txt
+
+## arXiv
+
+Single file:
+
+ ./fatcat_import.py arxiv /srv/fatcat/datasets/arxiv_raw_oai_snapshot_2019-05-22/2007-12-31-00000001.xml
+
+Bulk (one file per process):
+
+ fd .xml /srv/fatcat/datasets/arxiv_raw_oai_snapshot_2019-05-22/ | parallel -j15 ./fatcat_import.py arxiv {}
+
+## PubMed
+
+Run single:
+
+ time ./fatcat_import.py pubmed /srv/fatcat/datasets/pubmed_medline_baseline_2019/pubmed19n0400.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt
+
+ real 13m21.756s
+ user 9m10.720s
+ sys 0m14.100s
+
+Bulk:
+
+ # very memory intensive to parse these big XML files, so need to limit parallelism
+ fd .xml /srv/fatcat/datasets/pubmed_medline_baseline_2019 | time parallel -j3 ./fatcat_import.py pubmed {} /srv/fatcat/datasets/ISSN-to-ISSN-L.txt
+
## Matched
These each take 2-4 hours: