850ee002a1ce7707a2e86f9b3a1f534d514f6cd8 max Wed Mar 31 02:25:29 2021 -0700 updating blat servers table in gbic, refs #27301 diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh index 4d9eff1..889dfbd 100755 --- src/product/installer/browserSetup.sh +++ src/product/installer/browserSetup.sh @@ -1146,33 +1146,32 @@ # setup the mysql databases for the genome browser and grant # user access rights function mysqlDbSetup () { # ------------------- # Mysql db setup # ------------------- echo2 echo2 Creating Mysql databases customTrash, hgTemp and hgcentral waitKey $MYSQL -e 'CREATE DATABASE IF NOT EXISTS customTrash;' $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgcentral;' $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgTemp;' $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgFixed;' # empty db needed for gencode tracks - downloadFile http://$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");' + + updateBlatServers echo2 echo2 "Will now grant permissions to browser database access users:" echo2 "User: 'browser', password: 'genome' - full database access permissions" echo2 "User: 'readonly', password: 'access' - read only access for CGI binaries" echo2 "User: 'readwrite', password: 'update' - readwrite access for hgcentral DB" waitKey # Full access to all databases for the user 'browser' # This would be for browser developers that need read/write access # to all database tables. $MYSQL -e "CREATE USER browser@localhost IDENTIFIED BY 'genome';" $MYSQL -e "GRANT SELECT, INSERT, UPDATE, DELETE, FILE, "\ "CREATE, DROP, ALTER, CREATE TEMPORARY TABLES on *.* TO browser@localhost; " @@ -1617,30 +1616,38 @@ echo2 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr' waitKey downloadFile $UDRURL > /usr/local/bin/udr chmod a+x /usr/local/bin/udr fi } 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");' +} + 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/* } function updateBrowser { cgiUpdate echo @@ -1654,30 +1661,32 @@ echo updating GBDB: $DBS for db in $DBS; do echo2 syncing gbdb: $db rsync -avp $RSYNCOPTS $HGDOWNLOAD::gbdb/$db/ $GBDBDIR/$db/ done # update the mysql DBs stopMysql DBS=`ls /var/lib/mysql/ | egrep -v '(Trash$)|(hgTemp)|(^ib_)|(^ibdata)|(^aria)|(^mysql)|(performance)|(.flag$)|(hgcentral)'` for db in $DBS; do echo2 syncing full mysql database: $db $RSYNC --update --progress -avp $RSYNCOPTS $HGDOWNLOAD::mysql/$db/ $MYSQLDIR/$db/ done startMysql + updateBlatServers + echo2 update finished } function addTools { rsync -avP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ /usr/local/bin/ echo2 The UCSC User Tools were copied to /usr/local/bin echo2 Please note that most of the tools require an .hg.conf file in the users echo2 home directory. A very minimal .hg.conf file can be found here: echo2 "http://genome-source.soe.ucsc.edu/gitlist/kent.git/blob/master/src/product/minimal.hg.conf" } # ------------ end of utility functions ---------------- # -- START OF SCRIPT --- MAIN ---