.svnignore

+var

Makefile

+# The top level makefile. Targets like "all" and "clean"
+# are defined in the RULES file.
+
+TOP = .
+SUBDIRS = src
+
+include $(TOP)/tools/make/RULES_DM
+

bin/dm-ant

+#!/bin/sh
+
+# Run ant
+
+if [ -z $DM_ROOT_DIR ]; then
+    cd `dirname $0` && myDir=`pwd`
+    setupFile=$myDir/../../setup.sh
+    if [ ! -f $setupFile ]; then
+        echo "Cannot find setup file: $setupFile"
+        exit 1
+    fi
+    source $setupFile
+fi
+
+DM_HOST_ARCH=`uname | tr [A-Z] [a-z]`-`uname -m`
+export JAVA_HOME=$DM_SUPPORT_DIR/java/$DM_HOST_ARCH
+export ANT_HOME=$DM_SUPPORT_DIR/ant
+export PATH=$ANT_HOME/bin:$PATH
+ant $@
+
+

doc/RELEASE_NOTES.txt

+Release 20140930 (09/30/2014)
+=============================
+
+- Implemented first version of Web Portal UI: contains login page, and 
+  users/experiment type management pages
+- Developed project infrastructure tools: build scripts, web app configuration
+  and deployment scripts
+

etc/dm.deploy.conf

+DM_DB_NAME=dm
+DM_DB_USER=dm
+DM_DB_PASSWORD=dm
+DM_DB_HOST=127.0.0.1
+DM_DB_PORT=11136
+DM_DB_ADMIN_USER=postgres
+DM_DB_ADMIN_PASSWORD=
+DM_DB_ADMIN_HOSTS="127.0.0.1"
+DM_DB_CHARACTER_SET=utf8
+DM_DB_SCRIPTS_DIR=
+DM_CONTEXT_ROOT=dm
+

etc/dm.fsService.log.conf

+# Logging Configuration File
+#
+#
+# Available sections: 
+#  [LoggerLevels]       : lists regular levelregex to match against loggers.
+#  [ConsoleLogging]     : configures logging onto screen
+#  [FileLogging]        : configures logging into local file
+
+# The root key describes the root
+# logger level which is the default level for all loggers.
+
+# Level regular expressions (levelregex) are matched top down with the first
+# match setting the effective level. If no matches are found, default applies.  
+
+# Available logger levels: debug, info, warn, error, critical
+
+# In order for a message to be emitted by a specific handler the level of
+# the message must be greater than or equal to both the logger level and
+# the handler level.
+#
+
+# Example: Debug level for DbManager, info for everything else
+# 
+# [LoggerLevels]
+# levelregex: ^.*$=info
+#     ^DbManager$=debug
+#
+
+[LoggerLevels]
+root=error
+levelregex: ^.*$=debug
+
+#[ConsoleLogging]
+#handler=ConsoleLoggingHandler(sys.stdout,)
+#level=debug
+#format=%(asctime)s,%(msecs)003d %(levelname)s %(filename)s:%(lineno)d %(process)d:  %(message)s
+#dateformat=%Y-%m-%d %H:%M:%S
+
+# Custom log files can be setup here using config section [FileLogging<name>] 
+[FileLogging]
+handler=TimedRotatingFileLoggingHandler('/home/sveseli/Work/DM/dev/var/log/dm.fsService.log')
+level=debug
+format=%(asctime)s,%(msecs)003d %(levelname)s %(filename)s:%(lineno)d %(process)d:  %(message)s
+dateformat=%Y-%m-%d %H:%M:%S
+

etc/dm.log.conf

+# Logging Configuration File
+#
+#
+# Available sections: 
+#  [LoggerLevels]       : lists regular levelregex to match against loggers.
+#  [ConsoleLogging]     : configures logging onto screen
+#  [FileLogging]        : configures logging into local file
+
+# The root key describes the root
+# logger level which is the default level for all loggers.
+
+# Level regular expressions (levelregex) are matched top down with the first
+# match setting the effective level. If no matches are found, default applies.  
+
+# Available logger levels: debug, info, warn, error, critical
+
+# In order for a message to be emitted by a specific handler the level of
+# the message must be greater than or equal to both the logger level and
+# the handler level.
+#
+
+# Example: Debug level for DbManager, info for everything else
+# 
+# [LoggerLevels]
+# levelregex: ^.*$=info
+#     ^DbManager$=debug
+#
+
+[LoggerLevels]
+root=error
+levelregex: ^.*$=debug
+
+[ConsoleLogging]
+handler=ConsoleLoggingHandler(sys.stdout,)
+level=debug
+format=%(asctime)s,%(msecs)003d %(levelname)s %(filename)s:%(lineno)d %(process)d:  %(message)s
+dateformat=%Y-%m-%d %H:%M:%S
+
+# Custom log files can be setup here using config section [FileLogging<name>] 
+[FileLogging]
+handler=TimedRotatingFileLoggingHandler('/home/sveseli/Work/DM/dev/var/log/dm.log')
+level=debug
+format=%(asctime)s,%(msecs)003d %(levelname)s %(filename)s:%(lineno)d %(process)d:  %(message)s
+dateformat=%Y-%m-%d %H:%M:%S
+

etc/init.d/dm-fs-service

+#!/bin/sh
+
+#
+# dm-fs-service
+#
+# Starts the DM FileSystem Service
+#
+# chkconfig: 345 98 98
+# description: controls DM FileSystem Service
+
+### BEGIN INIT INFO
+# Provides: dm-fs-service
+# Required-Start: $local_fs dm-postgresql
+# Required-Stop: $local_fs
+# Default-Start:  2 3 4 5
+# Default-Stop: 0 1 6
+# Description: controls DM FileSystem Service
+### END INIT INFO
+
+# Source function library.
+. /etc/rc.d/init.d/functions
+
+# For SELinux we need to use 'runuser' not 'su'
+SU=su
+if [ -x /sbin/runuser ]; then
+    SU=runuser
+fi
+
+# Check if we are root before running command
+runCommand() {
+    _cmd="$@"
+    echo "COMMAND: $_cmd"
+    if [ `id -u` = 0 ]; then
+        $SU -l $DM_USER -c "_$cmd" 
+    else
+        eval "$_cmd" 
+    fi
+}
+
+# Set defaults for configuration variables
+if [ -z $DM_ROOT_DIR ]; then
+    myDir=`dirname $0`
+    currentDir=`pwd` && cd $myDir/../..
+    export DM_ROOT_DIR=`pwd`
+    cd $currentDir
+fi
+DM_SETUP_FILE=$DM_ROOT_DIR/setup.sh
+if [ ! -f $DM_SETUP_FILE ]; then
+    echo "Setup file $DM_SETUP_FILE does not exist."
+    exit 2
+fi
+. $DM_SETUP_FILE > /dev/null
+
+mkdir -p ${DM_ROOT_DIR}/var/run
+mkdir -p ${DM_ROOT_DIR}/var/log
+
+#DM_USER=dm
+DM_USER=`whoami`
+DM_PORT=22236   # 222-DM
+DM_HOST=0.0.0.0
+DAEMON_CMD=${DM_ROOT_DIR}/lib/python/dm/fs_service/service/fsService.py
+DAEMON_NAME="DmFsService"
+PIDFILE=${DM_ROOT_DIR}/var/run/dm_fs_service.pid
+DAEMON_ARGS="-d -p $PIDFILE --port $DM_PORT --host $DM_HOST --n-server-threads 12"
+export DM_LOG_CONFIG_FILE=${DM_ROOT_DIR}/etc/dm.fsService.log.conf
+
+# Determine SSL flags:
+#   DM_SERVICE_PROTOCOL=https
+#   DM_SERVICE_SSL_CERT_FILE=<cert path>
+#   DM_SERVICE_SSL_KEY_FILE=<key path>
+#   DM_SSL_CA_CERT_FILE=<ca cert path> (enables checking client certificates)
+
+if [ "$DM_SERVICE_PROTOCOL" = "https" ]; then
+    if [ -z "$DM_SERVICE_SSL_CERT_FILE" ]; then
+        echo "Cannot start service using SSL: DM_SERVICE_SSL_CERT_FILE is not defined." && exit 2
+    fi
+    if [ -z "$DM_SERVICE_SSL_KEY_FILE" ]; then
+        echo "Cannot start service using SSL: DM_SERVICE_SSL_KEY_FILE is not defined." && exit 2
+    fi
+    DAEMON_ARGS="$DAEMON_ARGS -c $DM_SERVICE_SSL_CERT_FILE -k $DM_SERVICE_SSL_KEY_FILE"
+
+    # Client certificate will be checked if DM_SSL_CA_CERT_FILE is provided.
+    if [ ! -z "$DM_SSL_CA_CERT_FILE" ]; then
+        DAEMON_ARGS="$DAEMON_ARGS -C $DM_SSL_CA_CERT_FILE"
+    fi
+fi
+
+RETVAL=0
+start() {
+    # Check if service is already running
+    status -p $PIDFILE > /dev/null 2>&1
+    if [ $? -ne 0 ]; then
+        echo -n $"Starting $DAEMON_NAME daemon: "   
+        runCommand ${DAEMON_CMD} ${DAEMON_ARGS}
+        RETVAL=$?
+        [ $RETVAL -eq 0 ] &&  success $"$DAEMON_NAME startup" || failure $"$DAEMON_NAME startup"
+        echo
+    fi
+    return $RETVAL
+}
+
+stop() {
+    status -p $PIDFILE > /dev/null 2>&1
+    if [ $? -eq 0 ]; then
+        echo -n $"Stopping $DAEMON_NAME daemon: "
+        PID=`cat $PIDFILE`
+        kill $PID
+        RETVAL=$?
+        [ $RETVAL -eq 0 ] && rm -f $PIDFILE && success $"$DAEMON_NAME shutdown" || failure $"$DAEMON_NAME shutdown"
+        echo
+    fi
+    return $RETVAL
+}
+
+restart() {
+    stop
+    start
+}
+
+case "$1" in
+    start)
+        start
+        ;;
+    stop)
+        stop
+        ;;
+    restart)
+        restart
+        ;;
+    status)
+        status -p $PIDFILE "$DAEMON_NAME"
+        RETVAL=$?
+        ;;
+    *)
+        echo $"Usage: $0 {start|stop|status|restart}"
+        RETVAL=2
+esac
+
+exit $RETVAL

etc/init.d/dm-glassfish

+#! /bin/sh
+### BEGIN INIT INFO
+# Provides:          glassfish
+# Required-Start:    $remote_fs $network $syslog
+# Required-Stop:     $remote_fs $network $syslog
+# Default-Start:     2 3 4 5
+# Default-Stop:      0 1 6
+# Short-Description: Starts GlassFish
+# Description:       Starts GlassFish application server
+### END INIT INFO
+
+# Source function library.
+. /etc/rc.d/init.d/functions
+
+# Source networking configuration.
+. /etc/sysconfig/network
+
+# Set root to default if needed.
+MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
+if [ -z "${DM_ROOT_DIR}" ]; then
+    DM_ROOT_DIR=$MY_DIR/../..
+fi
+        
+# Source environment file.
+DM_USER=`id -nu`
+DM_HOST=`hostname -s`
+DM_ENV_FILE=${DM_ROOT_DIR}/setup.sh
+if [ ! -f ${DM_ENV_FILE} ]; then
+    echo "Environment file ${DM_ENV_FILE} does not exist." 
+    exit 2
+fi
+. ${DM_ENV_FILE} > /dev/null
+
+export AS_JAVA=$DM_SUPPORT_DIR/java/$DM_HOST_ARCH
+DM_GLASSFISH_DIR=$DM_SUPPORT_DIR/glassfish/$DM_HOST_ARCH
+DERBY_DIR=$DM_SUPPORT_DIR/glassfish/$DM_HOST_ARCH/javadb/bin
+
+DM_DAEMON_NAME=glassfish
+DM_DAEMON_CONTROL_CMD=$DM_GLASSFISH_DIR/bin/asadmin
+DM_DAEMON_START_ARGS="start-domain domain1"
+DM_DAEMON_STOP_ARGS="stop-domain domain1"
+DM_DAEMON_STATUS_CMDS="uptime list-domains list-applications list-jdbc-resources"
+
+start() {
+    echo -n $"Starting ${DM_DAEMON_NAME}: "       
+    # Check if we're a privileged user
+    if [ `id -u` = 0 -a ${DM_USER} != "root" ]; then
+        su -m -c "${DM_DAEMON_CONTROL_CMD} ${DM_DAEMON_START_ARGS}" ${DM_USER}
+    else
+        ${DM_DAEMON_CONTROL_CMD} ${DM_DAEMON_START_ARGS}
+    fi
+    RETVAL=$?
+    [ $RETVAL -eq 0 ] && success $"${DM_DAEMON_NAME} startup" || failure $"${DM_DAEMON_NAME} startup"
+    echo
+}
+
+stop() {
+    echo -n $"Stopping ${DM_DAEMON_NAME}: "       
+    # Check if we're a privileged user
+    if [ `id -u` = 0 -a ${DM_USER} != "root" ]; then
+        su -m -c "${DM_DAEMON_CONTROL_CMD} ${DM_DAEMON_STOP_ARGS}" ${DM_USER}
+    else
+        ${DM_DAEMON_CONTROL_CMD} ${DM_DAEMON_STOP_ARGS}
+    fi
+    RETVAL=$?
+    [ $RETVAL -eq 0 ] && success $"${DM_DAEMON_NAME} shutdown" || failure $"${DM_DAEMON_NAME} shutdown"
+    echo
+}
+
+status() {
+    # Check if we're a privileged user
+    if [ `id -u` = 0 -a ${DM_USER} != "root" ]; then
+        for cmd in ${DM_DAEMON_STATUS_CMDS}; do
+            su -m -c "${DM_DAEMON_CONTROL_CMD} ${cmd}" ${DM_USER}
+        done
+    else
+        for cmd in ${DM_DAEMON_STATUS_CMDS}; do
+            ${DM_DAEMON_CONTROL_CMD} ${cmd}
+        done
+    fi
+}
+
+case "$1" in
+    start)
+        start
+    ;;
+    stop)
+        stop
+    ;;
+    restart)
+        stop
+        start
+    ;;
+    status)
+        status
+    ;;
+    *)
+        echo "Usage: $0 {start|stop|restart|status}"
+        exit 1
+    ;;
+esac
+
+

etc/init.d/dm-postgresql

+#!/bin/sh
+
+#
+# dm-postgresql 
+#
+# Starts the PostgreSQL server used for DM software
+# 
+# Modified from the original RHEL postgresql init.d script
+#
+# chkconfig: 345 97 97
+# description: controls Dm database server
+
+### BEGIN INIT INFO
+# Provides: dm-postgresql 
+# Required-Start: $local_fs
+# Required-Stop: $local_fs
+# Default-Start:  2 3 4 5
+# Default-Stop: 0 1 6
+# Description: controls Dm database server
+### END INIT INFO
+
+# PGVERSION is the full package version, e.g., 8.4.0
+PGVERSION=9.3.4
+# PGMAJORVERSION is major version, e.g., 8.4 (this should match PG_VERSION)
+PGMAJORVERSION=`echo "$PGVERSION" | sed 's/^\([0-9]*\.[0-9]*\).*$/\1/'`
+
+# Source function library.
+. /etc/rc.d/init.d/functions
+
+# Get function listing for cross-distribution logic.
+TYPESET=`typeset -f|grep "declare"`
+
+# Get config.
+. /etc/sysconfig/network
+
+# Find the name of the script
+# NAME=`basename $0`
+NAME="DM Database"
+
+# For SELinux we need to use 'runuser' not 'su'
+SU=su
+if [ -x /sbin/runuser ]; then
+    SU=runuser
+fi
+
+# Check if we are root before running command
+runCommand() {
+    _cmd="$@"
+    if [ `id -u` = 0 ]; then
+        $SU -l $PGUSER -c "_$cmd" >> $PGSTARTUPLOG 2>&1 < /dev/null
+    else
+        eval "$_cmd" >> $PGSTARTUPLOG 2>&1 < /dev/null
+    fi
+}
+
+
+# Set defaults for configuration variables
+if [ -z $DM_ROOT_DIR ]; then
+    myDir=`dirname $0`
+    currentDir=`pwd` && cd $myDir/../..
+    export DM_ROOT_DIR=`pwd`
+    cd $currentDir
+fi
+DM_SETUP_FILE=$DM_ROOT_DIR/setup.sh
+if [ ! -f $DM_SETUP_FILE ]; then
+    echo "Setup file $DM_SETUP_FILE does not exist."
+    exit 2
+fi
+. $DM_SETUP_FILE > /dev/null
+
+PGROOT=$DM_SUPPORT_DIR/postgresql/$DM_HOST_ARCH
+PGENGINE=$PGROOT/bin
+#PGUSER=dm
+PGUSER=`whoami`
+PGGROUP=`groups $PGUSER | cut -f3 -d ' '`
+PGPORT=11136    # 111-DM
+PGDATA=$PGROOT/data
+
+PGRUNDIR=$DM_ROOT_DIR/var/run
+PGLOGDIR=$DM_ROOT_DIR/var/log
+
+PGSTARTUPLOG=$PGLOGDIR/postgresql
+PGPIDFILE=$PGRUNDIR/postmaster.pid
+PGLOCKFILE=$PGRUNDIR/postmaster.lock
+
+mkdir -p $PGDATA && chown -R $PGUSER:$PGGROUP $PGDATA || exit 1
+mkdir -p $PGRUNDIR && chown -R $PGUSER:$PGGROUP $PGRUNDIR || exit 1
+mkdir -p $PGLOGDIR && chown -R $PGUSER:$PGGROUP $PGLOGDIR || exit 1
+
+export PGDATA
+export PGPORT
+export LD_LIBRARY_PATH=$PGROOT/lib
+
+# Check that networking is up.
+# Pretty much need it for postmaster.
+[ "${NETWORKING}" = "no" ] && exit 1
+
+[ -f "$PGENGINE/postmaster" ] || exit 1
+
+script_result=0
+
+start() {
+    PSQL_START=$"Starting ${NAME} service: "
+
+    # Make sure startup-time log file is valid
+    if [ ! -e "$PGSTARTUPLOG" -a ! -h "$PGSTARTUPLOG" ]; then
+        touch "$PGSTARTUPLOG" || exit 1
+        chown $PGUSER:$PGGROUP "$PGSTARTUPLOG"
+        chmod go-rwx "$PGSTARTUPLOG"
+        [ -x /sbin/restorecon ] && /sbin/restorecon "$PGSTARTUPLOG"
+    fi
+
+    # Check for the PGDATA structure
+    if [ -f "$PGDATA/PG_VERSION" ] && [ -d "$PGDATA/base" ]; then
+        # Check version of existing PGDATA
+        if [ x`cat "$PGDATA/PG_VERSION"` != x"$PGMAJORVERSION" ]; then
+            SYSDOCDIR="(Your System's documentation directory)"
+            echo
+            echo $"An old version of the database format was found."
+            echo $"You need to upgrade the data format before using PostgreSQL."
+            echo $"See $SYSDOCDIR/postgresql-$PGVERSION/README.rpm-dist for more information."
+            exit 1
+        fi
+
+    # No existing PGDATA! Warn the user to initdb it.
+    else
+        echo
+        echo "$PGDATA is missing. Use \"$0 initdb\" to initialize the cluster first."
+        echo_failure
+        echo
+        exit 1
+    fi
+
+    echo -n "$PSQL_START"
+    cmd="$PGENGINE/postmaster -p '$PGPORT' -D '$PGDATA' ${PGOPTS} &"
+    runCommand $cmd
+    sleep 2
+    pid=`pidof -s "$PGENGINE/postmaster"`
+    if [ $pid ] && [ -f "$PGDATA/postmaster.pid" ]; then
+        success "$PSQL_START"
+        touch $PGLOCKFILE
+        head -n 1 "$PGDATA/postmaster.pid" > $PGPIDFILE
+        echo
+    else
+        failure "$PSQL_START"
+        echo
+        script_result=1
+    fi
+}
+
+stop() {
+    echo -n $"Stopping ${NAME} service: "
+    cmd="export LD_LIBRARY_PATH=$LD_LIBRARY_PATH; $PGENGINE/pg_ctl stop -D '$PGDATA' -s -m fast" 
+    runCommand $cmd
+    ret=$? 
+    if [ $ret -eq 0 ]; then
+        echo_success
+    else
+        echo_failure
+        script_result=1
+    fi
+    echo
+    rm -f $PGPIDFILE
+    rm -f $PGLOCKFILE
+}
+
+restart() {
+    stop
+    start
+}
+
+condrestart() {
+    [ -e $PGLOCKFILE ] && restart
+}
+
+condstop() {
+    [ -e $PGLOCKFILE ] && stop
+}
+
+reload() {
+    cmd="export LD_LIBRARY_PATH=$LD_LIBRARY_PATH; $PGENGINE/pg_ctl reload -D '$PGDATA' -s" 
+    runCommand $cmd
+}
+
+initdb() {
+    if [ -f "$PGDATA/PG_VERSION" ]; then
+        echo -n "Data directory is not empty!"
+        echo_failure
+        echo
+        script_result=1
+    else
+        echo -n $"Initializing database: "
+        if [ ! -e "$PGDATA" -a ! -h "$PGDATA" ]; then
+            mkdir -p "$PGDATA" || exit 1
+            chown $PGUSER:$PGGROUP "$PGDATA"
+            chmod go-rwx "$PGDATA"
+        fi
+
+        # Clean up SELinux tagging for PGDATA
+        [ -x /sbin/restorecon ] && /sbin/restorecon "$PGDATA"
+
+        # Make sure the startup-time log file is OK, too
+        if [ ! -e "$PGSTARTUPLOG" -a ! -h "$PGSTARTUPLOG" ]; then
+            touch "$PGSTARTUPLOG" || exit 1
+            chown $PGUSER:$PGGROUP "$PGSTARTUPLOG"
+            chmod go-rwx "$PGSTARTUPLOG"
+            [ -x /sbin/restorecon ] && /sbin/restorecon "$PGSTARTUPLOG"
+        fi
+
+        # Initialize the database
+        cmd="$PGENGINE/initdb --pgdata='$PGDATA' --auth='ident'"
+        runCommand $cmd
+
+        # Create directory for postmaster log
+        mkdir -p "$PGDATA/pg_log"
+        chown $PGUSER:$PGGROUP "$PGDATA/pg_log"
+        chmod go-rwx "$PGDATA/pg_log"
+
+        if [ -f "$PGDATA/PG_VERSION" ]; then
+            echo_success
+        else
+            echo_failure
+            script_result=1
+        fi
+        echo
+    fi
+}
+
+# This script is slightly unusual in that the name of the daemon (postmaster)
+# is not the same as the name of the subsystem (postgresql)
+
+# See how we were called.
+case "$1" in
+    start)
+        start
+        ;;
+    stop)
+        stop
+        ;;
+    status)
+        status postmaster
+        script_result=$?
+        ;;
+    restart)
+        restart
+        ;;
+    condrestart)
+        condrestart
+        ;;
+    condstop)
+        condstop
+        ;;
+    reload|force-reload)
+        reload
+        ;;
+    initdb)
+        initdb
+        ;;
+    *)
+        echo $"Usage: $0 {start|stop|status|restart|condrestart|condstop|reload|force-reload|initdb}"
+        exit 1
+esac
+
+exit $script_result

lib/python

+../src/python
\ No newline at end of file

sbin/configure_dm_webapp.sh

+#!/bin/sh
+
+#
+# Script used for configuring DM webapp
+# Deployment configuration can be set in etc/$DM_DB_NAME.deploy.conf file
+#
+# Usage:
+#
+# $0 [DM_DB_NAME]
+#
+
+MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
+if [ -z "${DM_ROOT_DIR}" ]; then
+    DM_ROOT_DIR=$MY_DIR/..
+fi
+DM_ENV_FILE=${DM_ROOT_DIR}/setup.sh
+if [ ! -f ${DM_ENV_FILE} ]; then
+    echo "Environment file ${DM_ENV_FILE} does not exist." 
+    exit 2
+fi
+. ${DM_ENV_FILE} > /dev/null
+
+# Use first argument as db name, if provided
+DM_DB_NAME=${DM_DB_NAME:=dm}
+if [ ! -z "$1" ]; then
+    DM_DB_NAME=$1
+fi
+echo "Using DB name: $DM_DB_NAME"
+
+# Look for deployment file in etc directory, and use it to override
+# default entries
+deployConfigFile=$DM_ROOT_DIR/etc/${DM_DB_NAME}.deploy.conf
+if [ -f $deployConfigFile ]; then
+    echo "Using deployment config file: $deployConfigFile"
+    . $deployConfigFile
+else
+    echo "Deployment config file $deployConfigFile not found, using defaults"
+fi
+
+DM_HOST_ARCH=`uname | tr [A-Z] [a-z]`-`uname -m`
+GLASSFISH_DIR=$DM_SUPPORT_DIR/glassfish/$DM_HOST_ARCH
+JAVA_HOME=$DM_SUPPORT_DIR/java/$DM_HOST_ARCH
+
+export AS_JAVA=$JAVA_HOME
+ASADMIN_CMD=$GLASSFISH_DIR/bin/asadmin 
+
+DM_DB_HOST=${DM_DB_HOST:=localhost}
+DM_DB_PORT=${DM_DB_PORT:=11136}
+DM_DB_USER=${DM_DB_USER:=dm}
+DM_DB_PASSWORD=${DM_DB_PASSWORD:=dm}
+DM_DB_POOL=postgresql_${DM_DB_NAME}_DbPool
+DM_DATA_SOURCE=${DM_DB_NAME}_DataSource
+DM_DOMAIN=domain1
+
+# copy db driver
+echo "Copying db driver"
+rsync -ar $DM_ROOT_DIR/src/java/DmWebPortal/lib/postgresql-9.3-1102.jdbc41.jar $GLASSFISH_DIR/glassfish/domains/${DM_DOMAIN}/lib/ext
+
+# restart server
+echo "Restarting glassfish"
+$ASADMIN_CMD stop-domain ${DM_DOMAIN}
+$ASADMIN_CMD start-domain ${DM_DOMAIN}
+
+# create JDBC connection pool
+echo "Creating JDBC connection pool $DM_DB_POOL"
+$ASADMIN_CMD create-jdbc-connection-pool --datasourceclassname org.postgresql.ds.PGSimpleDataSource --restype javax.sql.DataSource --property user=${DM_DB_USER}:password=${DM_DB_PASSWORD}:driverClass="org.postgresql.Driver":portNumber=${DM_DB_PORT}:databaseName=${DM_DB_NAME}:serverName=${DM_DB_HOST}:url="jdbc\:postgresql\://${DM_DB_HOST}\:${DM_DB_PORT}/${DM_DB_NAME}" ${DM_DB_POOL}
+
+# create JDBC resource associated with this connection pool
+echo "Creating JDBC resource $DM_DATA_SOURCE"
+$ASADMIN_CMD create-jdbc-resource --connectionpoolid ${DM_DB_POOL} ${DM_DATA_SOURCE}
+
+# test the connection settings 
+echo "Testing connection"
+$ASADMIN_CMD ping-connection-pool $DM_DB_POOL || exit 1
+

sbin/create_dm_db.sh

+#!/bin/sh
+
+#
+# Script used for creating DM database
+# Deployment configuration can be set in etc/$DM_DB_NAME.deploy.conf file
+#
+# Usage:
+#
+# $0 [DM_DB_NAME [DM_DB_SCRIPTS_DIR]]
+#
+
+DM_DB_NAME=dm
+DM_DB_USER=dm
+DM_DB_PASSWORD=dm
+DM_DB_HOST=127.0.0.1
+DM_DB_PORT=11136
+DM_DB_ADMIN_USER=postgres
+DM_DB_ADMIN_HOSTS="127.0.0.1 bluegill1.aps.anl.gov visa%.aps.anl.gov"
+DM_DB_ADMIN_PASSWORD=
+DM_DB_CHARACTER_SET=utf8
+
+
+CURRENT_DIR=`pwd`
+MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
+cd $CURRENT_DIR
+
+if [ -z "${DM_ROOT_DIR}" ]; then
+    DM_ROOT_DIR=$MY_DIR/..
+fi
+DM_SQL_DIR=$DM_ROOT_DIR/db
+DM_RUN_DIR=$DM_ROOT_DIR/var/run
+DM_ENV_FILE=${DM_ROOT_DIR}/setup.sh
+if [ ! -f ${DM_ENV_FILE} ]; then
+    echo "Environment file ${DM_ENV_FILE} does not exist." 
+    exit 1
+fi
+. ${DM_ENV_FILE} > /dev/null 
+
+# DM_SUPPORT_DIR should now be defined.
+if [ -z "$DM_SUPPORT_DIR" ]; then
+    echo "Invalid environment file ${DM_ENV_FILE}: DM_SUPPORT_DIR is not defined."
+    exit 1
+fi
+PG_DIR=$DM_SUPPORT_DIR/postgresql/$DM_HOST_ARCH
+PG_CONTROL_SCRIPT=$DM_ROOT_DIR/etc/init.d/dm-postgresql
+PG_DATA_DIR=$PG_DIR/data
+PG_HBA_CONF=$PG_DATA_DIR/pg_hba.conf
+DB_LOCK_FILE=${DM_RUN_DIR}/${DM_DB_NAME}.db.lock
+DB_CREATE_SCRIPT=${DM_ROOT_DIR}/db/create_${DM_DB_NAME}_db.sql
+
+# Use first argument as db name, if provided
+if [ ! -z "$1" ]; then
+    DM_DB_NAME=$1
+fi
+echo "Using DB name: $DM_DB_NAME"
+
+# Look for deployment file in etc directory, and use it to override
+# default entries
+deployConfigFile=$DM_ROOT_DIR/etc/${DM_DB_NAME}.deploy.conf
+if [ -f $deployConfigFile ]; then
+    echo "Using deployment config file: $deployConfigFile"
+    . $deployConfigFile
+else
+    echo "Deployment config file $deployConfigFile not found, using defaults"
+fi
+
+# Second argument overrides directory with db population scripts
+DM_DB_SCRIPTS_DIR=${DM_DB_SCRIPTS_DIR:=$DM_SQL_DIR}
+if [ ! -z "$2" ]; then
+    DM_DB_SCRIPTS_DIR=$2
+fi
+if [ ! -d $DM_DB_SCRIPTS_DIR ]; then
+    echo "DB Scripts directory $DM_DB_SCRIPTS_DIR does not exist."
+    exit 1
+fi
+
+echo "Using DB scripts directory: $DM_DB_SCRIPTS_DIR"
+
+execute() {
+    msg="$@"
+    if [ ! -z "$DM_DB_ADMIN_PASSWORD" ]; then
+        sedCmd="s?$DM_DB_ADMIN_PASSWORD?\\*\\*\\*\\*\\*\\*?g"
+        echo "Executing: $@" | sed -e $sedCmd
+    else
+        echo "Executing: $@"
+    fi
+    eval "$@"
+}
+
+createDb() {
+    if [ -f $DB_LOCK_FILE ]; then
+        echo "Database lock file $DB_LOCK_FILE already exists, will not proceed."
+        return 1
+    fi
+    echo "Creating database $DM_DB_NAME"
+    ${PG_DIR}/bin/createdb -U $DM_DB_USER -h $DM_DB_HOST -p $DM_DB_PORT $DM_DB_NAME || return 1
+    echo "Creating database schema for $DM_DB_NAME"
+    ${PG_DIR}/bin/psql -U $DM_DB_USER -h $DM_DB_HOST -p $DM_DB_PORT -d $DM_DB_NAME -f $DB_CREATE_SCRIPT || return 1
+    touch $DB_LOCK_FILE
+}
+
+createDbUser() {
+    _dbUser=$1
+    shift 1
+    _createFlags=$@
+
+    # create user
+    ${PG_DIR}/bin/createuser -h $DM_DB_HOST -p $DM_DB_PORT $_createFlags $_dbUser || return 1
+}
+
+modifyDbUserPassword() {
+    _dbUser=$1
+    _dbPassword=$2
+    _tmpFile=/tmp/$$.sql
+    echo "alter user $_dbUser with password '$_dbPassword';" > $_tmpFile
+    $PG_DIR/bin/psql -h $DM_DB_HOST -p $DM_DB_PORT -d postgres -f $_tmpFile
+    rm -f $_tmpFile
+}
+
+# Check for failed earlier attempt
+if [ -f $PG_HBA_CONF.orig ]; then
+    echo "File $PG_HBA_CONF.orig exists, refusing to proceed."
+    exit 1
+fi
+
+# Initialize db if needed
+dbAction=restart
+createDbRootUser=false
+if [ ! -f $PG_HBA_CONF ]; then
+    $PG_CONTROL_SCRIPT initdb || exit 1
+    dbAction=start
+    createDbRootUser=true
+fi
+
+# Modify db permissions, restart db.
+echo "Modifying db access permissions"
+mv $PG_HBA_CONF $PG_HBA_CONF.orig
+cat $PG_HBA_CONF.orig | sed 's?host.*all.*all.*127.*?host all all 127.0.0.1/32 trust?g' | sed 's?host.*all.*all.*::1/128.*?host all all ::1/128 trust?g' > $PG_HBA_CONF || exit 1
+echo "Restarting database server"
+$PG_CONTROL_SCRIPT $dbAction
+
+# Create db root user if needed
+sttyOrig=`stty -g`
+if [ $createDbRootUser = "true" ]; then
+    # Read db password if needed 
+    if [ -z "$DM_DB_ADMIN_PASSWORD" ]; then
+        stty -echo
+        read -p "Enter DB password for the $DM_DB_ADMIN_USER (DB root) user: " DM_DB_ADMIN_PASSWORD
+        echo
+        stty $sttyOrig
+    fi
+
+    # Create postgres user 
+    echo "Creating $DM_DB_ADMIN_USER"
+    createDbUser $DM_DB_ADMIN_USER -E -s || exit 1
+    modifyDbUserPassword $DM_DB_ADMIN_USER $DM_DB_ADMIN_PASSWORD || exit 1
+fi
+
+# Read user db password if needed 
+if [ -z "$DM_DB_USER_PASSWORD" ]; then
+    stty -echo
+    read -p "Enter DB password for the $DM_DB_USER user: " DM_DB_USER_PASSWORD
+    echo
+    stty $sttyOrig
+fi
+
+# Create db user
+echo "Creating $DM_DB_USER"
+createDbUser $DM_DB_USER -E -d || exit 1
+modifyDbUserPassword $DM_DB_USER $DM_DB_USER_PASSWORD || exit 1
+
+# Create db
+echo "Creating database: $DM_DB_NAME"
+createDb || exit 1
+
+# populate db
+cd $CURRENT_DIR && cd $DM_DB_SCRIPTS_DIR
+DM_DB_TABLES="\
+  experiment_type \
+  user_info \
+  role_type \
+  user_system_role \
+  policy_type \
+  policy_property \
+  allowed_policy_value
+"
+for dbTable in $DM_DB_TABLES; do
+    dbFile=populate_$dbTable.sql
+    if [ -f $dbFile ]; then
+        echo "Populating $dbTable using $dbFile script"
+        execute ${PG_DIR}/bin/psql -U $DM_DB_USER -h $DM_DB_HOST -p $DM_DB_PORT -d $DM_DB_NAME -f $dbFile || exit 1
+    else
+        echo "$dbFile not found, skipping $dbTable update"
+    fi
+done
+
+# cleanup
+echo "Restoring db access permissions"
+if [ $createDbRootUser = "true" ]; then
+    # db was just created, enable password access
+    cat $PG_HBA_CONF.orig | sed 's?host.*all.*all.*127.*?host all all 127.0.0.1/32 md5?g' | sed 's?host.*all.*all.*::1/128.*?host all all ::1/128 md5?g' > $PG_HBA_CONF || exit 1
+    rm -f $PG_HBA_CONF.orig 
+else
+    # no changes needed to original hba file
+    mv $PG_HBA_CONF.orig $PG_HBA_CONF
+fi
+
+echo "Restarting database server"
+$PG_CONTROL_SCRIPT restart
+
+echo "Database $DM_DB_NAME created successfully"
+echo
+

sbin/deploy_dm_webapp.sh

+#!/bin/sh
+
+#
+# Script used for deploying DM webapp
+# Deployment configuration can be set in etc/$DM_DB_NAME.deploy.conf file
+#
+# Usage:
+#
+# $0 [DM_DB_NAME]
+#
+
+MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
+if [ -z "${DM_ROOT_DIR}" ]; then
+    DM_ROOT_DIR=$MY_DIR/..
+fi
+DM_ENV_FILE=${DM_ROOT_DIR}/setup.sh
+if [ ! -f ${DM_ENV_FILE} ]; then
+    echo "Environment file ${DM_ENV_FILE} does not exist." 
+    exit 2
+fi
+. ${DM_ENV_FILE} > /dev/null
+
+# Use first argument as db name, if provided
+DM_DB_NAME=${DM_DB_NAME:=dm}
+if [ ! -z "$1" ]; then
+    DM_DB_NAME=$1
+fi
+echo "Using DB name: $DM_DB_NAME"
+
+# Look for deployment file in etc directory, and use it to override
+# default entries
+deployConfigFile=$DM_ROOT_DIR/etc/${DM_DB_NAME}.deploy.conf
+if [ -f $deployConfigFile ]; then
+    echo "Using deployment config file: $deployConfigFile"
+    . $deployConfigFile
+else
+    echo "Deployment config file $deployConfigFile not found, using defaults"
+fi
+
+DM_HOST_ARCH=`uname | tr [A-Z] [a-z]`-`uname -m`
+DM_CONTEXT_ROOT=${DM_CONTEXT_ROOT:=dm}
+GLASSFISH_DIR=$DM_SUPPORT_DIR/glassfish/$DM_HOST_ARCH
+DM_DEPLOY_DIR=$GLASSFISH_DIR/glassfish/domains/domain1/autodeploy
+DM_DIST_DIR=$DM_ROOT_DIR/src/java/DmWebPortal/dist
+DM_BUILD_WAR_FILE=DmWebPortal.war
+DM_WAR_FILE=$DM_CONTEXT_ROOT.war
+JAVA_HOME=$DM_SUPPORT_DIR/java/$DM_HOST_ARCH
+
+if [ ! -f $DM_DIST_DIR/$DM_BUILD_WAR_FILE ]; then
+    echo "$DM_BUILD_WAR_FILE not found in $DM_DIST_DIR."
+    exit 1
+fi
+
+# Modify war file for proper context/persistence settings and
+# repackage it into new war 
+echo "Repackaging war file for context root $DM_CONTEXT_ROOT"
+cd $DM_DIST_DIR
+rm -rf $DM_CONTEXT_ROOT
+mkdir -p $DM_CONTEXT_ROOT
+cd $DM_CONTEXT_ROOT
+jar xf ../$DM_BUILD_WAR_FILE
+
+configFile=WEB-INF/glassfish-web.xml
+cmd="cat $configFile | sed 's?<context-root.*?<context-root>${DM_CONTEXT_ROOT}</context-root>?g' > $configFile.2 && mv $configFile.2 $configFile"
+eval $cmd
+
+configFile=WEB-INF/classes/META-INF/persistence.xml
+cmd="cat $configFile | sed 's?<jta-data-source.*?<jta-data-source>${DM_DB_NAME}_DataSource</jta-data-source>?g' > $configFile.2 && mv $configFile.2 $configFile"
+eval $cmd
+
+jar cf ../$DM_WAR_FILE *
+
+export AS_JAVA=$JAVA_HOME
+ASADMIN_CMD=$GLASSFISH_DIR/bin/asadmin
+
+# copy war file
+echo "Copying war file $DM_DIST_DIR/$DM_WAR_FILE to $DM_DEPLOY_DIR"
+rm -f $DM_DEPLOY_DIR/${DM_WAR_FILE}_*
+cp $DM_DIST_DIR/$DM_WAR_FILE $DM_DEPLOY_DIR
+
+# wait on deployment
+echo "Waiting on war deployment..."
+WAIT_TIME=30
+cd $DM_DEPLOY_DIR
+t=0
+while [ $t -lt $WAIT_TIME ]; do
+    sleep 1
+    deploymentStatus=`ls -c1 ${DM_WAR_FILE}_* 2> /dev/null | sed 's?.*war_??g'`
+    if [ ! -z "$deploymentStatus" ]; then
+        break
+    fi
+    t=`expr $t + 1`
+done
+echo "Deployment Status: $deploymentStatus"
+
+

sbin/destroy_all_dm_databases.sh

+#!/bin/sh
+
+#
+# Script used for destroying all DM databases
+#
+# Usage:
+#
+# $0 
+#
+
+DM_DB_NAME=dm
+DM_DB_USER=dm
+DM_DB_PASSWORD=dm
+DM_DB_HOST=127.0.0.1
+DM_DB_PORT=11136
+DM_DB_ADMIN_USER=postgres
+DM_DB_ADMIN_HOSTS="127.0.0.1 bluegill1.aps.anl.gov visa%.aps.anl.gov"
+DM_DB_ADMIN_PASSWORD=
+DM_DB_CHARACTER_SET=utf8
+
+
+CURRENT_DIR=`pwd`
+MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
+cd $CURRENT_DIR
+
+if [ -z "${DM_ROOT_DIR}" ]; then
+    DM_ROOT_DIR=$MY_DIR/..
+fi
+DM_SQL_DIR=$DM_ROOT_DIR/db
+DM_RUN_DIR=$DM_ROOT_DIR/var/run
+DM_ENV_FILE=${DM_ROOT_DIR}/setup.sh
+if [ ! -f ${DM_ENV_FILE} ]; then
+    echo "Environment file ${DM_ENV_FILE} does not exist." 
+    exit 1
+fi
+. ${DM_ENV_FILE} > /dev/null 
+
+# DM_SUPPORT_DIR should now be defined.
+if [ -z "$DM_SUPPORT_DIR" ]; then
+    echo "Invalid environment file ${DM_ENV_FILE}: DM_SUPPORT_DIR is not defined."
+    exit 1
+fi
+PG_DIR=$DM_SUPPORT_DIR/postgresql/$DM_HOST_ARCH
+PG_CONTROL_SCRIPT=$DM_ROOT_DIR/etc/init.d/dm-postgresql
+PG_DATA_DIR=$PG_DIR/data
+PG_HBA_CONF=$PG_DATA_DIR/pg_hba.conf
+DB_CREATE_SCRIPT=${DM_ROOT_DIR}/db/create_${DM_DB_NAME}_db.sql
+
+# Ask user to verify this action
+cd $DM_RUN_DIR
+lockFileList=`ls -c1 *.db.lock 2> /dev/null`
+
+if [ -z $lockFileList ]; then
+    echo "There are no active databases"
+else
+    dbNamelist=""
+    for lockFile in $lockFileList; do
+        dbName=`echo $lockFile | cut -f1 -d'.'`
+        dbNameList="$dbNameList $dbName"
+    done
+    echo "Found active databases: $dbNameList"
+    read -p "Proceed [y/N]? " proceedFlag
+    if [ "$proceedFlag" != "y" ]; then
+        echo "Active databases were not destroyed."
+        exit 1
+    fi
+fi
+
+# Stop db.
+$PG_CONTROL_SCRIPT stop
+
+# Remove db data directory
+echo "Removing database directory"
+rm -rf $PG_DATA_DIR
+
+# Remove lock files.
+if [ ! -z "$lockFileList" ]; then
+    echo "Removing lock files"
+    rm -f $lockFileList
+fi
+
+echo "Cleanup done"
+echo
+
+