Dumping Script

Basic flow:

Papers are dumped in a .ace file format to ? every ? On ? that are either a 20- or 30-something, the file is also copied to ? Every ? at ? am, a cronjob on spica copies the file from tazendra to spica into the Data_from_Kimberly directory.

The papers cronjob is on the acedb account : 0 2 * * thu /home/postgres/work/citace_upload/papers/wrapper.pl

The dumping script lives here:

/home/postgres/work/citace_upload/papers/dumpPapAce.pl

The papers.ace file is dumped automatically at 2am on the Thursday of the upload and copied to spica at 4am on that same Thursday.

The dumping script will check for any dead gene IDs attached to papers and comment them out of the .ace file until they are fixed/deleted from postgres by a curator.

The AQL query that finds all dead genes in WB is:

select all class gene where ->Species like "*elegans" and ->Status like "Dead"

The dumping script will also check that all associated genes are in the format: WBGenennnnnnnn where the 8 n's correspond to numbers.

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