writedb_entry

#!/bin/sh -
# 
# This script reads and writes entries from a database. 
# Examples:
# writedb_entry -help
# writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
#

args="$*"

PRG=$0
progname=`basename $0`

while [ -h "$PRG" ] ; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '.*/.*' > /dev/null; then
      PRG="$link"
  else
      PRG="`dirname $PRG`/$link"
  fi
done

ARTEMIS_HOME=`dirname "$PRG"`/..

CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.1-407.jdbc2ee.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH

# iBatis jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar
export CLASSPATH

FLAGS="-mx512m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
DEFAULT_CONNECTION="-Dchado=pathdbsrv1-dmz.sanger.ac.uk:5432/snapshot?genedb_ro -Dread_only"

if [ $# = 0 ]
then
    :
else
   while test $# != 0
       do
       case $1 in
       -Dchado*)
          DEFAULT_CONNECTION="$1" ;;
       -D*) 
          FLAGS="$FLAGS $1" ;;
       *) break ;;
       esac
       shift
   done
fi

echo starting to write with flags: $DEFAULT_CONNECTION $FLAGS 1>&2

java $DEFAULT_CONNECTION $FLAGS uk.ac.sanger.artemis.io.ReadAndWriteEntry $*