Index: src/utils/qa/findLevel.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/findLevel.csh,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 1000000 -r1.16 -r1.17
--- src/utils/qa/findLevel.csh	11 Apr 2009 00:37:03 -0000	1.16
+++ src/utils/qa/findLevel.csh	6 Jan 2010 23:20:13 -0000	1.17
@@ -1,286 +1,105 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ################################
 #  
 #  09-26-2007
 #  Ann Zweig
 #
 #  find out which level in the trackDb directory
 #  a track is on, and which level the corresponding
 #  .html file is on.
 #
 ################################
 
 
 set db=""
 set tableName=""
 set currDir=""
 set dbs=""
-set encode=""
-set split=""
-set partName=""
-set matches=""
-set match=""
-set prio=""
-set vis=""
 
-if ( $#argv < 2  || $#argv > 4 ) then
+if ( $#argv != 2 ) then
   echo
   echo " searches trackDb hierarchy for your table and corresponding .html file"
-  echo " optionally returns the location of the priority and visibility entries"
-  echo " returns the lowest-level directory for each" 
+  echo " also returns the value of the priority and visibility entries"
+  echo " and the .ra file location for each" 
   echo
-  echo "    usage:  database tableName [priority] [visibility]"
+  echo "    usage:  database tableName"
   echo
   exit
 else
   set db=$argv[1]
   set tableName=$argv[2]
 endif
 echo
 
-# find out if they want priority and/or visibility as well
-if ( $#argv == 3 ) then
-  if ( $argv[3] == 'priority' ) then
-    set prio="T"
-  endif
-  if ( $argv[3] == 'visibility' ) then
-    set vis="T"
-  endif
-endif
-if ( $#argv == 4 ) then
-  set prio="T"
-  set vis="T"
-endif
-
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 # make sure this is a valid database name
 set dbs=`hgsql -e "SELECT name FROM dbDb" hgcentraltest | grep -w $db`
 if ( "$dbs" != $db ) then
   echo
   echo "   Invalid database name.  Try again."
   echo
   exit
 endif
 
 # check for trackDb dir at $USER root
 file ~/trackDb | grep -q 'symbolic link'
 if ( $status ) then
   echo "\n  this program presumes you have a symlink to trackDb \
     in your home dir\n"
   exit
 else
   # start at the assembly level
   cd ~/trackDb/*/$db 
   set currDir=`pwd`
 endif
 
-# detect split chroms and check trackDb for db/table combination 
-set split=`getSplit.csh $db $tableName hgwdev`'_'
-hgsql -N -e 'SHOW TABLES' $db | egrep -wqi "${split}$tableName|$tableName"
-if ($status) then 
-  # look for ref to composite main entries which have no tables
-  find ../../ -name "trackDb*ra" | xargs grep -wq "subTrack.$tableName" 
-  if ($status) then
-    echo " ERROR: No such database/table combination: $db $tableName"
-    echo "  and no composite track by that name.\n"
-    exit
-  else
-    echo "  Composite track. No single table by this name: $tableName"
-    echo
-  endif
-else
-  find ../../ -name "trackDb*ra" | xargs grep -xq "track.$tableName" 
-  if ($status) then
-    echo "  This is a composite subtrack table"
-    echo
-  endif
-endif
-
-# check for entry in trackDb.ra, starting at assembly level
-set matches=`grep -ws "track.$tableName" trackDb.ra`
-set match=`echo $matches | grep -v "^#"`
-if ( "$match" != '' ) then
-  # the track is mentioned in the assembly-level trackDb.ra file
-else
-  # see if it's in another assembly-level trackDb*
-  set partName=`grep -wHs track.$tableName trackDb.*.ra`
-  if ( "$partName" != '' ) then
-    # the track is mentioned in an assembly-level trackDb.*.ra file
-    set encode=`echo $partName | sed -e "s/trackDb//" | sed -e "s/.ra:track $tableName//"`
-  else 
-    # the track is not at the assembly-level, go up to the organism level
-    cd ..
-    set currDir=`pwd`
-    set matches=`grep -ws track.$tableName trackDb.ra`
-    set match=`echo $matches | grep -v "^#"`
-    if ( "$match" != '' ) then
-      # the track is mentioned in the organism-level trackDb.ra file
-    else
-      # see if it's in another organism-level trackDb.*.ra
-      set partName=`grep -wHs track.$tableName trackDb.*.ra`
-      if ( "$partName" != '' ) then
-        # the track is mentioned in an organism-level trackDb.*.ra file
-        set encode=`echo $partName | sed -e "s/trackDb//" | sed -e "s/.ra:track $tableName//"`
-      else
-        # the track is not at the organism level, go up to the top level
-        cd ..
-        set currDir=`pwd`
-        set matches=`grep -ws track.$tableName trackDb.ra`
-        set match=`echo $matches | grep -v "^#"`
-        if ( "$match" != '' ) then
-          # the track is mentioned in the top-level trackDb.ra file
-        else 
-           # the track is not at the top level either - it does not exist
-           echo " * the $tableName track does not exist in any level trackDb.ra file"
-           set currDir=""
-        endif
-      endif
-    endif
-  endif
-endif
-if ($currDir != "") then
-  echo " * trackDb: \
-    `echo $currDir | sed -e 's^.*makeDb^~^'`/trackDb$encode.ra"
-endif
-echo
-
 ###########################################
-# now, find the level of the associated .html file
+# find the level of the associated .html file
 # start at the assembly level
 cd ~/trackDb/*/$db
 set currDir=`pwd`
 
 if (-e $tableName.html) then
   # the .html file is found at the assembly-level
 
 else
   # the .html is not found at the assembly-level, go up to the organism level
   cd ..
   set currDir=`pwd`
   if (-e $tableName.html) then
     # the .html file is found at the organism-level
 
   else
     # the .html file is not found at the organism level, go up to the top level
     cd ..
     set currDir=`pwd`
     if (-e $tableName.html) then
       # the .html file is found at the top-level
     else
       # the .html file is not at the top level either - it does not exist
       echo " * the $tableName.html file does not exist at any level"
       set currDir=""
     endif
   endif
 endif
 if ($currDir != "") then
   echo " * html file: \
     `echo $currDir | sed 's^.*makeDb^~^'`/$tableName.html"
 endif
 echo
 
-###########################################
-# check for entry in priority.ra file, starting at assembly level
-if ( "T" == $prio) then
-  # start back at the assembly level
-  cd ~/trackDb/*/$db 
-  set currDir=`pwd`
-  set matches=`grep -ws "track.$tableName" priority.ra`
-  set match=`echo $matches | grep -v "^#"`
-  if ( "$match" != '' ) then
-    # the track is mentioned in the assembly-level priority.ra file
-  else
-    # the track is not at the assembly-level, go up to the organism level
-    cd ..
-    set currDir=`pwd`
-    set matches=`grep -ws track.$tableName priority.ra`
-    set match=`echo $matches | grep -v "^#"`
-    if ( "$match" != '' ) then
-      # the track is mentioned in the organism-level priority.ra file
-    else
-      # the track is not at the organism level, go up to the top level
-      cd ..
-      set currDir=`pwd`
-      set matches=`grep -ws track.$tableName priority.ra`
-      set match=`echo $matches | grep -v "^#"`
-      if ( "$match" != '' ) the
-        # the track is mentioned in the top-level priority.ra file
-      else 
-        # the track is not at the top level either
-        echo " * priority:"
-        echo " The $db.$tableName track entry does not exist in any level"
-        echo " priority.ra file. This doesn't mean there is no priority"
-        echo " entry -- it's probably in the trackDb.ra file."
-        set currDir=""
-      endif
-    endif
-  if ($currDir != "") then
-    if (-e $currDir/priority.ra) then
-      echo " * priority: \
-        `echo $currDir | sed -e 's^.*makeDb^~^'`/priority.ra"
-    else
-      echo " * priority:"
-      echo " The $db.$tableName track entry does not exist in any level"
-      echo " priority.ra file. This doesn't mean there is no priority"
-      echo " entry -- it's probably in the trackDb.ra file."
-    endif
-  endif
-  echo
-endif #end find priority entry
 
 ###########################################
-# check for entry in visibility.ra file, starting at assembly level
-if ( "T" == $vis) then
-  # start back at the assembly level
-  cd ~/trackDb/*/$db 
-  set currDir=`pwd`
-  set matches=`grep -ws "track.$tableName" visibility.ra`
-  set match=`echo $matches | grep -v "^#"`
-  if ( "$match" != '' ) then
-    # the track is mentioned in the assembly-level visibility.ra file
-  else
-    # the track is not at the assembly-level, go up to the organism level
-    cd ..
-    set currDir=`pwd`
-    set matches=`grep -ws track.$tableName visibility.ra`
-    set match=`echo $matches | grep -v "^#"`
-    if ( "$match" != '' ) then
-      # the track is mentioned in the organism-level visibility.ra file
-    else
-      # the track is not at the organism level, go up to the top level
-      cd ..
-      set currDir=`pwd`
-      set matches=`grep -ws track.$tableName visibility.ra`
-      set match=`echo $matches | grep -v "^#"`
-      if ( "$match" != '' ) the
-        # the track is mentioned in the top-level visibility.ra file
-      else 
-        # the track is not at the top level either
-        echo " * visibility:"
-        echo " The $db.$tableName track entry does not exist in any level"
-        echo " visibility.ra file. This doesn't mean there is no visibility"
-        echo " entry -- it's probably in the trackDb.ra file."
-        set currDir=""
-      endif
-    endif
-  if ($currDir != "") then
-    if (-e $currDir/visibility.ra) then
-      echo " * visibility: \
-        `echo $currDir | sed -e 's^.*makeDb^~^'`/visibility.ra"
-    else
-      echo " * visibility:"
-      echo " The $db.$tableName track entry does not exist in any level"
-      echo " visibility.ra file. This doesn't mean there is no visibility"
-      echo " entry -- it's probably in the trackDb.ra file."
-    endif
-  endif
-  echo
-endif #end find visibility entry
+# find the trackDb.ra entry (using tdbQuery)
+
+echo " * trackDb:"
+tdbQuery "select track,priority,visibility,filePos from $db" \
+ | grep -w -A3 "$tableName"
 
 exit 0

