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| author | Martin Czygan <martin.czygan@gmail.com> | 2021-09-10 09:47:32 +0200 |
|---|---|---|
| committer | Martin Czygan <martin.czygan@gmail.com> | 2021-09-10 09:47:32 +0200 |
| commit | 72c2f524e68b74645ea549466d4215d1b675063e (patch) | |
| tree | b0a265700a483e51dda3e9ac739bbf9e7510badd | |
| parent | 23a7a0d537871427f8fe0bccc8074b3936d52d9b (diff) | |
| download | refcat-72c2f524e68b74645ea549466d4215d1b675063e.tar.gz refcat-72c2f524e68b74645ea549466d4215d1b675063e.zip | |
tasks: sort needs a tmpdir
| -rw-r--r-- | python/refcat/techreport.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/python/refcat/techreport.py b/python/refcat/techreport.py index 4223d18..4fe5771 100644 --- a/python/refcat/techreport.py +++ b/python/refcat/techreport.py @@ -20,10 +20,11 @@ class COCIDOIOnly(Refcat): tail -n +2 | cut -d , -f2,3 | perl -F, -lane 'printf qq[%s\n], join ",", sort @F' | - LC_ALL=C sort -S25% | + LC_ALL=C sort -T {tmpdir} -S25% | zstd -c -T0 > {output} """, - input=self.input().path) + input=self.input().path, + tmpdir=self.tmpdir) luigi.LocalTarget(output).move(self.output().path) def output(self): @@ -43,10 +44,11 @@ class BrefDOIOnly(Refcat): parallel --pipe -j 24 --block 10M "jq -R -rc 'fromjson? | [.source_doi, .target_doi] | @tsv'" | tr $'\t' ',' | perl -F, -lane 'printf qq[%s\n], join ",", sort @F' | - LC_ALL=C sort -S25% | + LC_ALL=C sort -T {tmpdir} -S25% | zstd -c -T0 > {output} """, - input=self.input().path) + input=self.input().path, + tmpdir=self.tmpdir) luigi.LocalTarget(output).move(self.output().path) def output(self): |