5adcf6bc2904690de7b7b30a83ec8a7a0996abe9 galt Tue Aug 21 00:01:25 2018 -0700 changing cse subdomain to soe diff --git src/utils/qa/showTracks src/utils/qa/showTracks index ba80861..ae0ec59 100755 --- src/utils/qa/showTracks +++ src/utils/qa/showTracks @@ -1,331 +1,331 @@ #! /bin/tcsh echo "Content-Type:text/html" echo echo "<HTML>" echo "<HEAD>" 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 <br>" echo '<TITLE>Track UI on '`echo $srvr | sed "s/.ucsc.edu//" \ - | sed "s/.cse//"`' </TITLE>' + | sed "s/.soe//"`' </TITLE>' echo "</HEAD>" echo echo "<BODY>" echo echo '<H2>Track UI on '`echo $srvr | sed "s/.ucsc.edu//" \ - | sed "s/.cse//"`'</H2>' + | sed "s/.soe//"`'</H2>' # echo "Hello.<br><br>" echo "<BLOCKQUOTE><B> 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 + set node=hgw${machine}.soe endif echo '<A HREF="showTracks?srvr='$node'.ucsc.edu">' endif echo $machine | sed "s/genome/RR/" echo "</A> " end echo " </B>" echo "</BLOCKQUOTE>" 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<br>" 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: $sql <br>" exit 0 endif #echo "$grpraw <br>" 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 <br>" end #echo "<br>" #echo "grpname: size $#grpname = $grpname <br>" #echo "grplabel: size $#grplabel= $grplabel <br>" #echo "<br>" #echo "<br>" set sql = 'select name from dbDb where active = "1" and name not like "zoo%" order by orderKey;' set dblist = `/cluster/bin/$MACHTYPE/hgsql -h mysqlbeta hgcentralbeta -B --skip-column-names -e "$sql"` set err = $status if ($err) then echo "error $err processing: $sql <br>" exit 0 endif #echo $dblist #foreach db ( $dblist ) # echo "$db <br>" #end #echo "<br>" #echo "<br>" set sql = 'drop table gbjunk;' #echo "$sql<br>" /cluster/bin/$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: $sql <br>" endif #echo "got past table cleanup.<br>" set sql = '' set sql = "$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 "$sql<br>" #debug remove #echo "$sql<br>" #echo "$user<br>" #echo "$pwd<br>" #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 <br>" exit 0 endif #echo "got past table create.<br>" 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: $sql <br>" exit 0 endif end #echo "<br>" #echo "<br>" set sql = 'load data local infile "'"$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 <br>" exit 0 endif #echo "got past table load.<br>" rm -f $junkPath # ==== MAIN LOOP =========== @ g = 1 while ( $g <= $#grplabel ) set lbl = `echo $grplabel[$g] | sed -e "s/_/ /g"` echo "<H3>$lbl</H3>" # ---- FIND ALL TRACKS IN GRP g ---- @ trkdone = 0 @ trkchunk = 50 set sql = 'select count(distinct shortLabel, ".", tableName) from gbjunk ' set sql = "$sql"'where grp="'"$grpname[$g]"'" ' #echo "$sql<br>" set trkcount = `/cluster/bin/$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: $sql <br>" exit 0 endif #echo "trkcount=$trkcount<br>" echo "<table BORDER CELLSPACING=0 CELLPADDING=5>" #-- column headings -- echo "<th>" echo "Track" echo "</th>" foreach db ( $dblist ) echo "<th>" echo "$db" echo "</th>" 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 "$sql<br>" set trklist = `/cluster/bin/$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: $sql <br>" exit 0 endif #echo "$trklist<br>" echo "<br>" #-- do rows -- while ("$trklist" != "") echo "<tr>" echo "<td>" set shortLabel = "" set sep = "" while ("$trklist[1]" != ".") #echo "$trklist[1] " set shortLabel = "$shortLabel$sep$trklist[1]" shift trklist set sep = " " end shift trklist echo "$shortLabel" echo "</td>" #get table too for yes links set table = "$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 "$sql<br>" set datalist = `/cluster/bin/$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: $sql <br>" exit 0 endif #echo "$datalist<br>" foreach db ( $dblist ) echo "<td>" #echo "$db" set found = "0" foreach dl ( $datalist ) if ("$dl" == "$db") then set found = "1" endif end if ( "$found" == "1" ) then set link = '<a href="http://'"$srvr"'/cgi-bin/hgTrackUi' set link = "$link"'?db='"$db"'&g='"$table"'&c=chr1&position=chr1:1-10000' set link = "$link"'" target=_blank>yes</a>' echo "$link" else echo "no" endif echo "</td>" end #--------------------------------- echo "</tr>" end @ trkdone = $trkdone + $trkchunk end echo "</table>" # ---------------------------------- @ g = $g + 1 end echo "<br>" echo "<br>" set sql = 'drop table gbjunk;' #echo "$sql<br>" /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 <br>" exit 0 endif #echo "got past table cleanup.<br>" #echo "The End.<br>" #echo "<br>" # ==== END MAIN LOOP =========== echo echo "</BODY>" echo "</HTML>"