91cecec4e65aa52dfa528d17a1fba9e1b7672381 lrnassar Tue Jun 4 13:41:15 2019 -0700 Updating scripts to point to new beta machine #23616 diff --git src/utils/qa/showTracks src/utils/qa/showTracks index ae0ec59..371014b 100755 --- src/utils/qa/showTracks +++ src/utils/qa/showTracks @@ -1,16 +1,18 @@ #! /bin/tcsh +source `which qaConfig.csh` + 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. @@ -60,31 +62,31 @@ 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 grpraw = `/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta $recentDb -B --skip-column-names -e "$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 $grpraw[1]) shift grpraw @@ -94,148 +96,148 @@ set txt = "$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 "$sql"` +set dblist = `/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta hgcentralbeta -B --skip-column-names -e "$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 "$sql" +/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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'" +#echo "/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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" +/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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" >> $junkPath + /cluster/bin/$MACHTYPE/hgsql -h $sqlbeta $db -B --skip-column-names -e "$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" +/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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 "$sql"` + set trkcount = `/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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 "$sql"` + set trklist = `/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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 ("$trklist" != "") echo "<tr>" echo "<td>" set shortLabel = "" @@ -249,31 +251,31 @@ shift trklist echo "$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 datalist = `/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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 @@ -300,31 +302,31 @@ 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" +/cluster/bin/$MACHTYPE/hgsql -h $sqlbeta -u$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>"