#! /bin/tcsh echo "Content-Type:text/html" echo echo "" echo "" set srvr = "genome.ucsc.edu" if ( $?QUERY_STRING == 0 ) then set QUERY_STRING = "srvr=genome.ucsc.edu" endif if ( "$QUERY_STRING" == "" ) then set QUERY_STRING = "srvr=genome.ucsc.edu" endif # Split the field=value pair on the '='. set pair=`echo $QUERY_STRING | sed 's/=/\t/'` # The first part of the pair is the name. set varname=`echo ${pair} | awk '{print $1}'` # The second part of the pair is the srvr name. set varval=`echo ${pair} | awk '{print $2}'` if ("$varname" == "srvr") then set srvr = "$varval" endif #echo "dbg: pair = $pair
" echo 'Track UI on '`echo $srvr | sed "s/.ucsc.edu//" \ | sed "s/.cse//"`' ' echo "" echo echo "" echo echo '

Track UI on '`echo $srvr | sed "s/.ucsc.edu//" \ | sed "s/.cse//"`'

' # echo "Hello.

" echo "
hgw:  " # display without a link if that's the page you are on. foreach machine ( dev beta genome 1 2 3 4 5 6 7 8 ) echo $srvr | grep $machine > /dev/null if ( $status ) then if ( $machine == RR || $machine == genome) then set node=genome set machine=RR else set node=hgw${machine}.cse endif echo '' endif echo $machine | sed "s/genome/RR/" echo " " end echo " " echo "
" set line=`grep "pq.user" hg.conf` set pair=`echo $line| sed 's/=/\t/'` set user=`echo ${pair} | awk '{print $2}'` set line=`grep "pq.password" hg.conf` set pair=`echo $line| sed 's/=/\t/'` set pwd=`echo ${pair} | awk '{print $2}'` set junkPath = "../trash/gbjunk" # normal cgi use #set junkPath = "./gbjunk" # use when running from commandline set recentDb = "hg17" set sql = 'select name, label, "." from grp ' set sql = "$sql"'where name not like "user" and name not like "encode" and name not like "x" ' set sql = "$sql"'order by priority;' #echo "$sql
" set grpraw = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta $recentDb -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "$grpraw
" set grpname = () set grplabel = () while ( "$grpraw" != "" ) #echo "$grpraw[1] = " set grpname = ($grpname $grpraw[1]) shift grpraw set txt = "" set sep = "" while ( "$grpraw[1]" != "." ) set txt = "$txt$sep$grpraw[1]" shift grpraw set sep = "_" end shift grpraw set grplabel = ($grplabel "$txt") #echo "$txt
" end #echo "
" #echo "grpname: size $#grpname = $grpname
" #echo "grplabel: size $#grplabel= $grplabel
" #echo "
" #echo "
" set sql = 'select name from dbDb where active = "1" and name not like "zoo%" order by orderKey;' set dblist = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta hgcentralbeta -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo $dblist #foreach db ( $dblist ) # echo "$db
" #end #echo "
" #echo "
" set sql = 'drop table gbjunk;' #echo "$sql
" /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql" set err = $status if ($err) then # ignore this error, probably the table doesn't exist because it got cleaned up #echo "error $err processing: $sql
" endif #echo "got past table cleanup.
" set sql = '' set sql = "$sql"'create table gbjunk(' set sql = "$sql"'db varchar(255), ' set sql = "$sql"'grp varchar(255), ' set sql = "$sql"'tableName varchar(255), ' set sql = "$sql"'shortLabel varchar(255));' #echo "$sql
" #debug remove #echo "$sql
" #echo "$user
" #echo "$pwd
" #echo "/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e '$sql'" /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql" set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "got past table create.
" rm -f $junkPath foreach db ( $dblist ) set sql = 'select "'"$db"'", grp, tableName, shortLabel from trackDb ' set sql = "$sql"'where grp not like "user" and grp not like "encode" and grp not like "x" ' set sql = "$sql"'order by grp;' /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta $db -B --skip-column-names -e "$sql" >> $junkPath set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif end #echo "
" #echo "
" set sql = 'load data local infile "'"$junkPath"'" into table gbjunk;' /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -e "$sql" set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "got past table load.
" rm -f $junkPath # ==== MAIN LOOP =========== @ g = 1 while ( $g <= $#grplabel ) set lbl = `echo $grplabel[$g] | sed -e "s/_/ /g"` echo "

$lbl

" # ---- FIND ALL TRACKS IN GRP g ---- @ trkdone = 0 @ trkchunk = 50 set sql = 'select count(distinct shortLabel, ".", tableName) from gbjunk ' set sql = "$sql"'where grp="'"$grpname[$g]"'" ' #echo "$sql
" set trkcount = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "trkcount=$trkcount
" echo "" #-- column headings -- echo "" foreach db ( $dblist ) echo "" end while ( $trkdone < $trkcount ) set sql = 'select distinct shortLabel, ".", tableName from gbjunk ' set sql = "$sql"'where grp="'"$grpname[$g]"'" ' set sql = "$sql"'order by shortLabel ' set sql = "$sql"'limit '"$trkdone"', '"$trkchunk" #echo "$sql
" set trklist = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "$trklist
" echo "
" #-- do rows -- while ("$trklist" != "") echo "" echo "" #get table too for yes links set table = "$trklist[1]" shift trklist #-------DB COLUMNS LOOP----------- set sql = 'select db from gbjunk ' set sql = "$sql"'where grp="'"$grpname[$g]"'" ' set sql = "$sql"'and shortLabel="'"$shortLabel"'" ' set sql = "$sql"'order by db;' #echo "$sql
" set datalist = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "$datalist
" foreach db ( $dblist ) echo "" end #--------------------------------- echo "" end @ trkdone = $trkdone + $trkchunk end echo "
" echo "Track" echo "" echo "$db" echo "
" set shortLabel = "" set sep = "" while ("$trklist[1]" != ".") #echo "$trklist[1] " set shortLabel = "$shortLabel$sep$trklist[1]" shift trklist set sep = " " end shift trklist echo "$shortLabel" echo "" #echo "$db" set found = "0" foreach dl ( $datalist ) if ("$dl" == "$db") then set found = "1" endif end if ( "$found" == "1" ) then set link = 'yes' echo "$link" else echo "no" endif echo "
" # ---------------------------------- @ g = $g + 1 end echo "
" echo "
" set sql = 'drop table gbjunk;' #echo "$sql
" /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta -u$user -p$pwd qapushq -B --skip-column-names -e "$sql" set err = $status if ($err) then echo "error $err processing: $sql
" exit 0 endif #echo "got past table cleanup.
" #echo "The End.
" #echo "
" # ==== END MAIN LOOP =========== echo echo "" echo ""