--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/setup/asadmin-setup.sh	Tue Sep 08 17:00:21 2015 +0200
@@ -0,0 +1,212 @@
+#!/bin/bash
+# STOP!
+# DO NOT ADD MORE ASADMIN COMMANDS TO THIS SCRIPT!
+# IF YOU NEED TO ADD MORE GLASSFISH CONFIG SETTINGS, ADD THEM 
+# TO THE ../installer/glassfish-setup.sh SCRIPT. 
+# I'M ASSUMING THAT WE'LL WANT TO CONTINUE MAINTAINING THIS SCRIPT, 
+# (FOR VAGRANT SETUPS, etc.?); IT SHOULD STILL BE WORKING, BY 
+# CALLING THE NEW SCRIPT ABOVE - SO NO NEED TO DUPLICATE THE ASADMIN 
+# COMMANDS HERE. 
+# FROM NOW ON, ONLY NON-ASADMIN CONFIGURATION SHOULD GO INTO THIS 
+# SCRIPT. (which makes the name especially misleading - but I didn't 
+# want to change it, in case other scripts are calling it by name!)
+#     -Leonid 4.0 beta
+
+# This is a setup script for setting up Glassfish 4 to run Dataverse
+# The script was tested on Mac OS X.9
+# ASSUMPTIONS
+# * Script has to run locally (i.e. on the machine that hosts the server)
+# * Internet connectivity is assumed, in order to get the postgresql driver.
+
+##
+# Default values - Change to suit your machine.
+DEFAULT_GLASSFISH_ROOT=/Applications/NetBeans/glassfish-4.0
+DEFAULT_DOMAIN=domain1
+DEFAULT_ASADMIN_OPTS=" "
+
+###
+# Database values. Update as needed.
+# Note: DB_USER "dvnApp" is case-sensitive and later used in "scripts/database/reference_data.sql"
+#
+DB_PORT=5432; export DB_PORT
+DB_HOST=localhost; export DB_HOST
+DB_NAME=dvndb; export DB_NAME
+DB_USER=dvnApp; export DB_USER
+DB_PASS=dvnAppPass; export DB_PASS
+
+###
+# Rserve configuration: 
+RSERVE_HOST=localhost; export RSERVE_HOST
+RSERVE_PORT=6311; export RSERVE_PORT
+RSERVE_USER=rserve; export RSERVE_USER
+RSERVE_PASS=rserve; export RSERVE_PASS
+
+###
+# Other configuration values: 
+MEM_HEAP_SIZE=1024; export MEM_HEAP_SIZE
+HOST_ADDRESS=localhost; export HOST_ADDRESS
+SMTP_SERVER=mail.hmdc.harvard.edu; export SMTP_SERVER
+FILES_DIR=${HOME}/dataverse/files; export FILES_DIR
+
+### End of default configuration values.
+
+# "${VAR+xxx}" for unset vs. empty per http://stackoverflow.com/questions/228544/how-to-tell-if-a-string-is-not-defined-in-a-bash-shell-script/230593#230593
+
+if [ "${DB_NAME_CUSTOM+xxx}" ]
+ then
+  echo "Default DB_NAME ($DB_NAME) overridden: $DB_NAME_CUSTOM"
+  DB_NAME=$DB_NAME_CUSTOM
+fi
+
+if [ "${DB_USER_CUSTOM+xxx}" ]
+ then
+  echo "Default DB_USER ($DB_USER) overridden: $DB_USER_CUSTOM"
+  DB_USER=$DB_USER_CUSTOM
+fi
+
+if [ "${DB_PASS_CUSTOM+xxx}" ]
+ then
+  echo "Default DB_PASS ($DB_PASS) overridden: $DB_PASS_CUSTOM"
+  DB_PASS=$DB_PASS_CUSTOM
+fi
+
+#echo "end"
+#exit
+
+## 
+# External dependencies
+PGSQL_DRIVER_URL=http://jdbc.postgresql.org/download/postgresql-9.3-1100.jdbc41.jar
+
+if [ "$SUDO_USER" = "vagrant" ]
+  then
+  echo "We are running in a Vagrant environment."
+  cat /etc/redhat-release
+  # Choosing all lower case indentifiers for DB_NAME and DB_USER for this reason:
+  #
+  # Quoting an identifier also makes it case-sensitive, whereas unquoted names
+  # are always folded to lower case. For example, the identifiers FOO, foo, and
+  # "foo" are considered the same by PostgreSQL, but "Foo" and "FOO" are
+  # different from these three and each other. (The folding of unquoted names
+  # to lower case in PostgreSQL is incompatible with the SQL standard, which
+  # says that unquoted names should be folded to upper case. Thus, foo should
+  # be equivalent to "FOO" not "foo" according to the standard. If you want to
+  # write portable applications you are advised to always quote a particular
+  # name or never quote it.) --
+  # http://www.postgresql.org/docs/9.3/static/sql-syntax-lexical.html
+  DB_NAME=dataverse_db
+  DB_USER=dataverse_app
+  DB_PASS=secret
+  echo "Configuring EPEL Maven repo "
+  cd /etc/yum.repos.d
+  wget http://repos.fedorapeople.org/repos/dchen/apache-maven/epel-apache-maven.repo
+  cd
+  echo "Installing dependencies via yum"
+  yum install -y -q java-1.7.0-openjdk-devel postgresql-server apache-maven httpd mod_ssl
+  rpm -q postgresql-server
+  echo "Starting PostgreSQL"
+  chkconfig postgresql on
+  /sbin/service postgresql initdb
+  cp -a /var/lib/pgsql/data/pg_hba.conf /var/lib/pgsql/data/pg_hba.conf.orig
+  sed -i -e 's/ident$/trust/' /var/lib/pgsql/data/pg_hba.conf
+  /sbin/service postgresql start
+  POSTGRES_USER=postgres
+  echo "Creating database user $DB_USER"
+  su $POSTGRES_USER -s /bin/sh -c "psql -c \"CREATE ROLE \"$DB_USER\" UNENCRYPTED PASSWORD '$DB_PASS' NOSUPERUSER CREATEDB CREATEROLE NOINHERIT LOGIN\""
+  #su $POSTGRES_USER -s /bin/sh -c "psql -c '\du'"
+  echo "Creating database $DB_NAME"
+  su $POSTGRES_USER -s /bin/sh -c "psql -c 'CREATE DATABASE \"$DB_NAME\" WITH OWNER = \"$DB_USER\"'"
+  GLASSFISH_USER=glassfish
+  echo "Ensuring Unix user '$GLASSFISH_USER' exists"
+  useradd $GLASSFISH_USER || :
+  GLASSFISH_ZIP=`ls /downloads/glassfish*zip`
+  GLASSFISH_USER_HOME=~glassfish
+  echo "Copying $GLASSFISH_ZIP to $GLASSFISH_USER_HOME and unzipping"
+  su $GLASSFISH_USER -s /bin/sh -c "cp $GLASSFISH_ZIP $GLASSFISH_USER_HOME"
+  su $GLASSFISH_USER -s /bin/sh -c "cd $GLASSFISH_USER_HOME && unzip -q $GLASSFISH_ZIP"
+  DEFAULT_GLASSFISH_ROOT=$GLASSFISH_USER_HOME/glassfish4
+  su $GLASSFISH_USER -s /bin/sh -c "/scripts/installer/glassfish-setup.sh"
+fi
+
+
+# Set the scripts parameters (if needed)
+if [ -z "${GLASSFISH_ROOT+xxx}" ]
+ then
+  echo setting GLASSFISH_ROOT to $DEFAULT_GLASSFISH_ROOT
+  GLASSFISH_ROOT=$DEFAULT_GLASSFISH_ROOT; export GLASSFISH_ROOT
+fi
+if [ ! -d "$GLASSFISH_ROOT" ]
+  then
+    echo Glassfish root '$GLASSFISH_ROOT' does not exist
+    exit 1
+fi
+GLASSFISH_BIN_DIR=$GLASSFISH_ROOT/bin
+
+if [ -z "${DOMAIN+xxx}" ]
+  then
+    echo setting DOMAIN to $DEFAULT_DOMAIN
+    DOMAIN=$DEFAULT_DOMAIN
+    # setting the environmental variable GLASSFISH_DOMAIN, 
+    # for the ../installer/glassfish-setup.sh script, that runs 
+    # all the required asadmin comands
+    GLASSFISH_DOMAIN=$DOMAIN; export GLASSFISH_DOMAIN
+fi
+DOMAIN_DIR=$GLASSFISH_ROOT/glassfish/domains/$DOMAIN
+if [ ! -d "$DOMAIN_DIR" ]
+  then
+    echo Domain directory '$DOMAIN_DIR' does not exist
+    exit 2
+fi
+if [ -z "$ASADMIN_OPTS" ]
+ then
+  ASADMIN_OPTS=$DEFAULT_ASADMIN_OPTS; export ASADMIN_OPTS
+fi
+
+echo "Setting up your glassfish4 to support Dataverse"
+echo "Glassfish directory: "$GLASSFISH_ROOT
+echo "Domain directory:    "$DOMAIN_DIR
+
+###
+# getting the postgres driver
+DOMAIN_LIB=$DOMAIN_DIR/lib
+if ! grep -qs postgres $DOMAIN_LIB/*
+  then
+    DRIVER_NAME=$(echo $PGSQL_DRIVER_URL | tr / \\n | tail -n1)
+    echo Downloading postgresql driver '$DRIVER_NAME'
+    wget $PGSQL_DRIVER_URL -O $DOMAIN_LIB/$DRIVER_NAME
+  else
+    echo postgresql driver already installed.
+fi
+
+if [ "$SUDO_USER" = "vagrant" ]
+  then
+  /scripts/installer/glassfish-setup.sh
+  echo "Done configuring Vagrant environment"
+  exit 0
+fi
+
+###
+# Move to the glassfish dir
+pushd $GLASSFISH_BIN_DIR
+
+###
+# take the domain up, if needed.
+DOMAIN_DOWN=$(./asadmin list-domains | grep "$DOMAIN " | grep "not running")
+if [  $(echo $DOMAIN_DOWN|wc -c) -ne 1  ];
+  then
+    echo Trying to start domain $DOMAIN up...
+    ./asadmin $ASADMIN_OPTS start-domain $DOMAIN
+  else
+    echo domain running
+fi
+
+# ONCE AGAIN, ASADMIN COMMANDS BELOW HAVE ALL BEEN MOVED INTO scripts/installer/glassfish-setup.sh
+
+# TODO: diagnostics
+
+###
+# Clean up
+popd
+
+echo "Glassfish setup complete"
+date
+