db6167f2bb6f7e666e48290a919254cb9f93b3cd
max
  Wed Mar 20 07:49:33 2024 -0700
GBIC version: protecting blatservers table against duplicates created by a future generation of engineers who are not as afraid to change things as we are, refs #33230

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index b80f4e9..0a64e33 100644
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -1901,30 +1901,32 @@
 
 function cleanTrash () 
 {
     echo2 Removing files older than one day in $TRASHDIR, not running on $TRASHDIR/ct
     # -L = follow symlinks
     # -atime +1 = files older than one day
     find -L $TRASHDIR -not -path $TRASHDIR/ct/\* -and -type f -atime +1 -exec rm -f {} \;
 }
 
 function updateBlatServers ()
 {
    echo2 Creating or updating the BLAT servers table
    downloadFile http://$HGDOWNLOAD/admin/hgcentral.sql | $MYSQL hgcentral
    # the blat servers don't have fully qualified dom names in the download data
    $MYSQL hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".soe.ucsc.edu");'
+   # just in case that we ever add fully qualified dom names
+   $MYSQL hgcentral -e 'UPDATE blatServers SET host=replace(host,".soe.ucsc.edu.soe.ucsc.edu", ".soe.ucsc.edu");'
 }
 
 function cgiUpdate ()
 {
    # update the CGIs
    $RSYNC -avzP --exclude=RNAplot --exclude=hg.conf --exclude=hg.conf.local --exclude=RNAplot $HGDOWNLOAD::cgi-bin/ $APACHEDIR/cgi-bin/ 
    # update the html docs
    echo2 Updating Apache htdocs
    $RSYNC -avzP --exclude=*.{bb,bam,bai,bw,gz,2bit,bed} --exclude=ENCODE --exclude=trash $HGDOWNLOAD::htdocs/ $APACHEDIR/htdocs/ 
    # assign all downloaded files to a valid user. 
    chown -R $APACHEUSER:$APACHEUSER $APACHEDIR/*
    updateBlatServers
 }
 
 function updateBrowser {