60a0b6cb901a9d420c748f4dede149803dcf5a3d
rhead
  Thu Sep 22 19:41:51 2011 -0700
Simplified checkGbdbDiffs.csh so that it looks for missing files in all of /gbdb instead of a subset. This was prompted by a daily cron job error on an assembly with an entry in the dbDb table but no matching /gbdb directory. Removing getGbdbBeta.csh, as it was only called by checkGbdbDiffs.csh. Read more of my ramblings in Redmine #402.
diff --git src/utils/qa/getGbdbBeta.csh src/utils/qa/getGbdbBeta.csh
deleted file mode 100755
index 422d322..0000000
--- src/utils/qa/getGbdbBeta.csh
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/bin/tcsh
-source `which qaConfig.csh`
-
-####################
-#  06-20-05 Robert Kuhn
-#
-#  Script to dump /gbdb files from beta
-#
-####################
-
-set filePath=""
-set db=""
-set todayDate=`date +%Y%m%d`
-
-if ($#argv != 1) then
-  echo
-  echo "  script to dump most /gbdb files from beta."
-  echo "    gets all assembly files except ci1 and zoo."
-  echo "    uses list of assemblies on beta."
-  echo "       also list hgFixed."
-  echo "    ignores files with Scaffold in the name "
-  echo "       unless a db that uses them is specified."
-  echo "    ignores: axtNetDp1, ci1, zoo, /sacCer1/sam."
-  echo
-  echo '      usage:  database or path (will use "all")'
-  echo
-  exit
-else
-  set filePath=$argv[1]
-  set outpath=`echo $filePath | sed -e 's/\//./'`
-  set      db=`echo $filePath | sed -e 's/\/.*//'`
-endif
-
-set output=$outpath.gbdb.out
-set output2=$outpath.gbdb.list
-  # echo "filePath = $filePath"
-  # echo "outpath  = $outpath"
-  # echo "db       = $db"
-  # echo "output   = $output"
-  # echo "output2  = $output2"
-
-rm -f $output
-rm -f $output2
-
-# get assembly list from beta
-hgsql -h $sqlbeta -N -e "SELECT name FROM dbDb" hgcentralbeta \
-   | sort | grep -v ci1 | grep -v zoo > xxAssembliesxx
-echo "all" >> xxAssembliesxx
-echo "genbank" >> xxAssembliesxx
-echo "hgFixed" >> xxAssembliesxx
-
-# error checking for db name on command line
-# flag set to 1 if $db is actually an assembly (or genbank, all or hgFixed)"
-set dbFlag=0
-foreach assembly (`cat xxAssembliesxx`)
-  # echo $assembly
-  if ($db == "$assembly") then
-    set dbFlag=1
-    break
-  endif
-end
-
-if ($dbFlag == "0") then
-  echo '\n  '$db' is not an active assembly. try another assembly name, or "all"'
-  echo
-  exit
-endif
-
-# get the files from beta
-rm -f xxfullListxx
-if ($db == "all") then
-  foreach assembly (`cat xxAssembliesxx | grep -v "all"`)
-    # do not check Kevin's voluminous /sacCer1/sam/* files:
-    if ( $assembly == "sacCer1" ) then
-      set yeDirs=`ssh hgwbeta ls /gbdb/$assembly | grep -wv sam`
-      foreach yedir ( $yeDirs )
-        ssh hgwbeta find /gbdb/$assembly/$yedir -type f -print \
-          | grep -vi Scaffold \
-          | grep -v axtNetDp1   | grep -v "sacCer1/sam/" > tempfile
-          # grep -v description | grep -v genbank \
-        cat tempfile >> xxfullListxx
-        cat tempfile
-        rm -f tempfile
-      end
-    else 
-      ssh hgwbeta find /gbdb/$assembly -type f -print | grep -vi Scaffold \
-         | grep -v axtNetDp1   | grep -v "sacCer1/sam/" > tempfile
-         # grep -v description | grep -v genbank \
-      cat tempfile >> xxfullListxx
-      cat tempfile
-      rm -f tempfile
-    endif
-  end
-else
-  if (-e /gbdb/$filePath) then
-    ssh hgwbeta find /gbdb/$filePath -type f -print \
-         | grep -v axtNetDp1   | grep -v "sacCer1/sam/" \
-         | grep -v description > xxfullListxx
-  else
-    echo "\n  directory /gbdb/$filePath does not exist\n"
-    exit
-  endif
-endif
-
-sort xxfullListxx > gbdb.$db.$todayDate
-mv gbdb.$db.$todayDate /usr/local/apache/htdocs-genecats/qa/test-results/gbdb
-
-# clean up
-rm -f xxAssembliesxx
-rm -f xxfullListxx
