Difference between revisions of "Paper Pipeline Scripts"
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=Ace File Generation= | =Ace File Generation= | ||
| + | '''Papers''' | ||
| + | |||
| + | Before dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates. | ||
| + | |||
| + | papers cronjob is on the acedb account : | ||
| + | 0 2 * * thu /home/postgres/work/citace_upload/papers/wrapper.pl | ||
| + | |||
| + | It creates a file at : | ||
| + | /home/postgres/work/citace_upload/papers/out/papers.ace.<date> | ||
| + | and symlinks it to : | ||
| + | /home/postgres/public_html/cgi-bin/data/papers.ace | ||
| + | so you can see it on the web at : | ||
| + | http://tazendra.caltech.edu/~postgres/cgi-bin/data/papers.ace | ||
| + | |||
| + | While the cronjob runs every thursday, the wrapper only dumps on days | ||
| + | that are 20something or 30something. | ||
| + | |||
| + | If you ever need to run it on a different week, try : | ||
| + | /home/postgres/work/citace_upload/papers/dumpPapAce.pl > /home/postgres/work/citace_upload/papers/out/papers.ace.<date> | ||
| + | rm /home/postgres/public_html/cgi-bin/data/papers.ace | ||
| + | ln -s /home/postgres/work/citace_upload/papers/out/papers.ace.<date> /home/postgres/public_html/cgi-bin/data/papers.ace | ||
| + | and then you can pick it up from spica by ssh-ing into it, cd to the | ||
| + | directory, remove the existing file, and : | ||
| + | wget "http://tazendra.caltech.edu/~postgres/cgi-bin/data/papers.ace" | ||
Revision as of 19:00, 21 November 2016
PMID Downloads and Paper Editor
- get_new_elegans_xml.pl - dowloads new xml records from daily PubMed search of 'elegans'
- resides here: /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/get_new_elegans_xml.pl
- pap_match.pm - processes the PubMed xml records based on actions in the paper_editor.cgi
- resides here: /home/postgres/work/pgpopulation/pap_papers/new_papers/pap_match.pm
Ace File Generation
Papers
Before dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates.
papers cronjob is on the acedb account : 0 2 * * thu /home/postgres/work/citace_upload/papers/wrapper.pl
It creates a file at :
/home/postgres/work/citace_upload/papers/out/papers.ace.<date>
and symlinks it to :
/home/postgres/public_html/cgi-bin/data/papers.ace
so you can see it on the web at :
http://tazendra.caltech.edu/~postgres/cgi-bin/data/papers.ace
While the cronjob runs every thursday, the wrapper only dumps on days that are 20something or 30something.
If you ever need to run it on a different week, try :
/home/postgres/work/citace_upload/papers/dumpPapAce.pl > /home/postgres/work/citace_upload/papers/out/papers.ace.<date> rm /home/postgres/public_html/cgi-bin/data/papers.ace ln -s /home/postgres/work/citace_upload/papers/out/papers.ace.<date> /home/postgres/public_html/cgi-bin/data/papers.ace
and then you can pick it up from spica by ssh-ing into it, cd to the directory, remove the existing file, and :
wget "http://tazendra.caltech.edu/~postgres/cgi-bin/data/papers.ace"
