diff --git a/etc/writedb_entry b/etc/writedb_entry new file mode 100755 index 0000000000000000000000000000000000000000..fd67a336f7a8516a34cbc4b7e9891a69a46ac5cf --- /dev/null +++ b/etc/writedb_entry @@ -0,0 +1,42 @@ +#!/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="$*" + +ARTEMIS_HOME=/software/pathogen/projects/artemis/current/ +ARTEMIS_HOME=/software/pathogen/projects/artemis/test/ + +CLASSPATH=$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 $*