src/utils/qa/showTracks 1.7
1.7 2010/04/13 08:03:26 galt
hack to keep it afloat, the list was getting too big and I had to fetch 50 record chunks at a time. probably need to be re-designed at some point now that ENCODE and other stuff is creating thousands of tracks where we used to have hundreds
Index: src/utils/qa/showTracks
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/showTracks,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/utils/qa/showTracks 11 Apr 2009 00:37:05 -0000 1.6
+++ src/utils/qa/showTracks 13 Apr 2010 08:03:26 -0000 1.7
@@ -1,6 +1,5 @@
#! /bin/tcsh
-source `which qaConfig.csh`
echo "Content-Type:text/html"
echo
echo "<HTML>"
echo "<HEAD>"
@@ -72,9 +71,9 @@
set sql = "$sql"'order by priority;'
#echo "$sql<br>"
-set grpraw = `/cluster/bin/i386/hgsql $recentDb -B --skip-column-names -e "$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: $sql <br>"
exit 0
@@ -106,9 +105,9 @@
#echo "<br>"
#echo "<br>"
set sql = 'select name from dbDb where active = "1" and name not like "zoo%" order by orderKey;'
-set dblist = `/cluster/bin/i386/hgsql hgcentralbeta -B --skip-column-names -e "$sql"`
+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: $sql <br>"
exit 0
@@ -123,9 +122,9 @@
set sql = 'drop table gbjunk;'
#echo "$sql<br>"
-/cluster/bin/i386/hgsql -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
# ignore this error, probably the table doesn't exist because it got cleaned up
#echo "error $err processing: $sql <br>"
@@ -137,10 +136,18 @@
set sql = "$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 "$sql<br>"
-/cluster/bin/i386/hgsql -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"
+#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
@@ -151,9 +158,9 @@
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/i386/hgsql $db -B --skip-column-names -e "$sql" >> $junkPath
+ /cluster/bin/$MACHTYPE/hgsql -h mysqlbeta $db -B --skip-column-names -e "$sql" >> $junkPath
set err = $status
if ($err) then
echo "error $err processing: $sql <br>"
exit 0
@@ -162,9 +169,9 @@
#echo "<br>"
#echo "<br>"
set sql = 'load data local infile "'"$junkPath"'" into table gbjunk;'
-/cluster/bin/i386/hgsql -u$user -p$pwd qapushq -e "$sql"
+/cluster/bin/$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
@@ -181,20 +188,22 @@
set lbl = `echo $grplabel[$g] | sed -e "s/_/ /g"`
echo "<H3>$lbl</H3>"
# ---- FIND ALL TRACKS IN GRP g ----
- set sql = 'select distinct shortLabel, ".", tableName from gbjunk '
+
+
+ @ trkdone = 0
+ @ trkchunk = 50
+ set sql = 'select count(distinct shortLabel, ".", tableName) from gbjunk '
set sql = "$sql"'where grp="'"$grpname[$g]"'" '
- set sql = "$sql"'order by shortLabel;'
#echo "$sql<br>"
- set trklist = `/cluster/bin/i386/hgsql -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"`
+ set trkcount = `/cluster/bin/$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: $sql <br>"
exit 0
endif
- #echo "$trklist<br>"
- echo "<br>"
+ #echo "trkcount=$trkcount<br>"
echo "<table BORDER CELLSPACING=0 CELLPADDING=5>"
#-- column headings --
@@ -206,8 +215,24 @@
echo "$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 ("$trklist" != "")
echo "<tr>"
@@ -235,9 +260,9 @@
set sql = "$sql"'where grp="'"$grpname[$g]"'" '
set sql = "$sql"'and shortLabel="'"$shortLabel"'" '
set sql = "$sql"'order by db;'
#echo "$sql<br>"
- set datalist = `/cluster/bin/i386/hgsql -u$user -p$pwd qapushq -B --skip-column-names -e "$sql"`
+ set datalist = `/cluster/bin/$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 <br>"
exit 0
@@ -269,8 +294,12 @@
echo "</tr>"
end
+ @ trkdone = $trkdone + $trkchunk
+
+ end
+
echo "</table>"
# ----------------------------------
@@ -282,9 +311,9 @@
set sql = 'drop table gbjunk;'
#echo "$sql<br>"
-/cluster/bin/i386/hgsql -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