--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DVN-web/installer/dvninstall/install~	Wed May 13 11:50:21 2015 +0200
@@ -0,0 +1,1183 @@
+#!/usr/bin/perl
+
+use Getopt::Long;
+use Socket; 
+use File::Copy;
+
+my( %opts ) = ( );
+my( $rez ) = GetOptions( \%opts, "pg_only!");
+
+my $postgresonly = 0; 
+
+my @CONFIG_VARIABLES = (); 
+
+unless ($opts{pg_only})
+{
+    @CONFIG_VARIABLES = (       
+	    'HOST_DNS_ADDRESS',
+	    'GLASSFISH_DIRECTORY',
+	    'MAIL_SERVER',
+
+	    'POSTGRES_SERVER',
+	    'POSTGRES_PORT',
+	    'POSTGRES_DATABASE',
+	    'POSTGRES_USER',
+	    'POSTGRES_PASSWORD',
+
+	    'RSERVE_HOST',
+	    'RSERVE_PORT',
+	    'RSERVE_USER',
+	    'RSERVE_PASSWORD'
+
+	    ); 
+}
+else 
+{
+    @CONFIG_VARIABLES = (       
+	    'POSTGRES_SERVER',
+	    'POSTGRES_PORT',
+	    'POSTGRES_DATABASE',
+	    'POSTGRES_USER',
+	    'POSTGRES_PASSWORD'
+	    ); 
+
+    $postgresonly = 1; 
+}
+
+my %CONFIG_DEFAULTS = 
+    (       
+	    'HOST_DNS_ADDRESS', '',
+	    'GLASSFISH_DIRECTORY', '/home/glassfish/glassfish',
+	    'MAIL_SERVER',      'localhost',
+
+	    'POSTGRES_SERVER',  'localhost',
+	    'POSTGRES_PORT',    5432,
+	    'POSTGRES_DATABASE','dvnDb',
+	    'POSTGRES_USER',    'postgres',
+	    'POSTGRES_PASSWORD','admin',
+
+	    'RSERVE_HOST',      'localhost',
+	    'RSERVE_PORT',      6311,
+	    'RSERVE_USER',      'rserve',
+	    'RSERVE_PASSWORD',  'rserve'
+
+	    ); 
+
+
+my %CONFIG_PROMPTS = 
+    (       
+	    'HOST_DNS_ADDRESS', 'Internet Address of your host',
+	    'GLASSFISH_DIRECTORY', 'Glassfish Directory', 
+	    'MAIL_SERVER', 'SMTP (mail) server to relay notification messages',
+
+	    'POSTGRES_SERVER',  'Postgres Server',
+	    'POSTGRES_PORT',    'Postgres Server Port',
+	    'POSTGRES_DATABASE','Name of the Postgres Database',
+	    'POSTGRES_USER',    'Name of the Postgres User',
+	    'POSTGRES_PASSWORD','Postgres user password',
+
+	    'RSERVE_HOST',      'Rserve Server',
+	    'RSERVE_PORT',      'Rserve Server Port',
+	    'RSERVE_USER',      'Rserve User Name',
+	    'RSERVE_PASSWORD',  'Rserve User Password'
+
+	    ); 
+
+# Supported Posstgres JDBC drivers: 
+# (have to be configured explicitely, so that Perl "taint" (security) mode 
+# doesn't get paranoid)
+
+my $POSTGRES_DRIVER_8_3 = "postgresql-8.3-603.jdbc4.jar";  
+#my $POSTGRES_DRIVER_8_4 = "postgresql-8.4-703.jdbc4.jar";
+my $POSTGRES_DRIVER_8_4 = "postgresql-8.3-603.jdbc4.jar";  
+my $POSTGRES_DRIVER_9_0 = "postgresql-9.0-802.jdbc4.jar";
+my $POSTGRES_DRIVER_9_1 = "postgresql-9.1-902.jdbc4.jar";
+
+
+# A few preliminary checks: 
+
+# user -- must be root: 
+
+$user_real = `who am i`; 
+chop $user_real; 
+$user_real =~s/ .*$//; 
+
+if ( $< != 0 ) 
+{
+    print STDERR "\nERROR: You must be logged in as root to run the installer.\n\n";
+    exit 1; 
+}
+
+# OS: 
+
+my $uname_out = `uname -a`; 
+
+# hostname: 
+
+my $hostname_from_cmdline = `hostname`; 
+chop $hostname_from_cmdline; 
+
+$CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} = $hostname_from_cmdline;
+
+
+print "\nWelcome to the DVN installer.\n";
+unless ($opts{pg_only}) 
+{
+    print "You will be guided through the process of setting up a NEW\n";
+    print "instance of the DVN application\n";
+} 
+else 
+{
+    print "You will be guided through the process of configuring the\n";
+    print "LOCAL instance of PostgreSQL database for use by the DVN\n";
+    print "application.\n";
+}
+
+my @uname_tokens = split (" ", $uname_out); 
+
+if ( $uname_tokens[0] eq "Darwin" )
+{
+    print "\nThis appears to be a MacOS X system; good.\n";
+    # TODO: check the OS version
+
+    $WORKING_OS = "MacOSX"; 
+}
+elsif ( $uname_tokens[0] eq "Linux" )
+{
+    if ( -f "/etc/redhat-release" )
+    {
+	print "\nThis appears to be a RedHat system; good.\n";
+	$WORKING_OS = "RedHat"; 
+	# TODO: check the distro version
+    }
+    else 
+    {
+	print "\nThis appears to be a non-RedHat Linux system;\n";
+	print "this installation *may* succeed; but we're not making any promises!\n";
+	$WORKING_OS = "Linux"; 
+    }
+} 
+else 
+{
+    print "\nWARNING: This appears to be neither a Linux or MacOS X system!\n";
+    print "This installer script will most likely fail. Please refer to the\n";
+    print "DVN Installers Guide for more information.\n\n";
+
+    $WORKING_OS = "Unknown";
+
+    print "Do you wish to continue?\n [y/n] ";
+
+
+    my $yesnocont = <>; chop $yesnocont;
+
+    while ( $yesnocont ne "y" && $yesnocont ne "n" )
+    {
+	print "Please enter 'y' or 'n'!\n";
+	print "(or ctrl-C to exit the installer)\n";
+	$yesnocont = <>; chop $yesnocont;
+    }
+
+    if ( $yesnocont eq "n" )
+    {
+	exit 0;
+    }
+
+}
+
+ ENTERCONFIG: 
+
+print "\n";
+print "Please enter the following configuration values:\n";
+print "(hit [RETURN] to accept the default value)\n";
+print "\n";
+
+for $ENTRY (@CONFIG_VARIABLES)
+{
+    print $CONFIG_PROMPTS{$ENTRY} . ": ";
+    print "[" . $CONFIG_DEFAULTS{$ENTRY} . "] ";
+
+    $user_entry = <>; 
+    chop $user_entry; 
+
+    if ($user_entry ne "")
+    {
+	$CONFIG_DEFAULTS{$ENTRY} = $user_entry;
+    }
+
+    print "\n";
+}
+
+# CONFIRM VALUES ENTERED: 
+
+
+print "\nOK, please confirm what you've entered:\n\n";
+
+for $ENTRY (@CONFIG_VARIABLES)
+{
+    print $CONFIG_PROMPTS{$ENTRY} . ": " . $CONFIG_DEFAULTS{$ENTRY} . "\n";
+}
+
+print "\nIs this correct? [y/n] ";
+
+
+my $yesno = <>; chop $yesno;  
+
+while ( $yesno ne "y" && $yesno ne "n" )
+{
+    print "Please enter 'y' or 'n'!\n";
+    print "(or ctrl-C to exit the installer)\n";
+    $yesno = <>; chop $yesno;  
+}
+
+if ( $yesno eq "n" )
+{
+    goto ENTERCONFIG; 
+}
+
+# VALIDATION/VERIFICATION OF THE CONFIGURATION VALUES:                                               
+# 1. VERIFY MAIL SERVER THEY CONFIGURED: 
+
+=pod
+
+unless ( $postgresonly )
+{
+
+    my ( $mail_server_iaddr, $mail_server__paddr, $mail_server_proto, $mail_server_status );
+
+    $mail_server_status = 1; 
+
+    unless ( $mail_server_iaddr = inet_aton($CONFIG_DEFAULTS{'MAIL_SERVER'}) )
+    {
+	print STDERR "Could not look up $CONFIG_DEFAULTS{'MAIL_SERVER'},\n";
+	print STDERR "the host you specified as your mail server.\n";
+	$mail_server_status = 0; 
+    }
+
+    if ($mail_server_status) {
+	$mail_server_paddr = sockaddr_in(25, $mail_server_iaddr);
+	$mail_server_proto = getprotobyname('tcp');
+
+	unless ( socket(SOCK, PF_INET, SOCK_STREAM, $mail_server_proto) &&
+		 connect(SOCK, $mail_server_paddr) ) 
+	{
+	    print STDERR "Could not establish connection to $CONFIG_DEFAULTS{'MAIL_SERVER'},\n";
+	    print STDERR "the address you provided for your Mail server.\n";
+	    print STDERR "Please select a valid mail server, and try again.\n\n";
+
+	    $mail_server_status = 0;
+	}
+    
+    }
+
+    close (SOCK); 
+
+    unless ($mail_server_status) 
+    {
+	goto ENTERCONFIG; 
+    }
+}
+=cut
+
+# 2. CHECK IF THE WAR FILE IS AVAILABLE:                                                                
+unless ( -f "appdeploy/dist/DVN-web.war" )
+{
+    print "\nWARNING: Can't find the project .war file in appdeploy/dist/!\n";
+    print "\tAre you running the installer in the right directory?\n";
+    print "\tHave you built the war file?\n";
+    print "\t(if not, build the project and run the installer again)\n";
+
+    exit 0;
+}
+
+# check the working (installer) dir:
+my $cwd; 
+chomp($cwd = `pwd`);
+
+# 2b. CHECK IF THE SQL TEMPLATE IS IN PLACE AND CREATE THE SQL FILE 
+
+$SQL_REFERENCE_DATA = "referenceData.sql"; 
+$SQL_REFERENCE_TEMPLATE = "referenceData.sql.TEMPLATE"; 
+
+unless ( -f $SQL_REFERENCE_TEMPLATE  )
+{
+    print "\nWARNING: Can't find .sql data template!\n"; 
+    print "(are you running the installer in the right directory?)\n";
+    
+    exit 0; 
+}
+
+open DATATEMPLATEIN, $SQL_REFERENCE_TEMPLATE || die $@; 
+open SQLDATAOUT, '>'.$SQL_REFERENCE_DATA || die $@;
+
+while( <DATATEMPLATEIN> )
+{
+    s/%POSTGRES_USER%/$CONFIG_DEFAULTS{'POSTGRES_USER'}/g;
+    print SQLDATAOUT $_; 
+}
+
+
+close DATATEMPLATEIN; 
+close SQLDATAOUT; 
+
+# 3. CHECK POSTGRES AVAILABILITY: 
+
+my $pg_local_connection = 0; 
+
+if ( $CONFIG_DEFAULTS{'POSTGRES_SERVER'} eq 'localhost' )
+{
+    $pg_local_connection = 1; 
+
+    # 3a. CHECK FOR USER postgres:
+
+    print "\nChecking system user \"postgres\"... ";
+
+    $POSTGRES_SYS_NAME = "postgres";
+    $POSTGRES_SYS_UID = (getpwnam ("postgres"))[2]; 
+
+    if ($POSTGRES_SYS_UID == undef) {
+	print STDERR "\nERROR: I haven't been able to find user \"postgres\" on the system!\n";
+	print STDERR "(TODO: prompt the user instead to supply an alternative username, if\n";
+	print STDERR "available)\n";
+
+	exit 1; 
+    } 
+
+    print "OK.\n";
+
+    # 3b. LOCATE THE EXECUTABLE:
+
+    $sys_path = $ENV{'PATH'}; 
+    @sys_path_dirs = split ( ":", $sys_path ); 
+
+    $psql_exec = ""; 
+
+    for $sys_path_dir ( @sys_path_dirs )
+    {
+	if ( -x $sys_path_dir . "/psql" ) 
+	{
+	    $psql_exec = $sys_path_dir; 
+	    last; 
+	}
+    }
+
+    $pg_major_version = 0; 
+    $pg_minor_version = 0; 
+
+    if ( $psql_exec eq "" && $WORKING_OS eq "MacOSX" )
+    {
+	for $pg_minor_version ( "1", "0" )
+	{
+	    if ( -x "/Library/PostgreSQL/9." . $pg_minor_version . "/bin/psql" ) 
+	    {
+		$pg_major_version = 9;
+		$psql_exec = "/Library/PostgreSQL/9." . $pg_minor_version . "/bin";
+		last; 
+	    }
+	}
+	if (!$pg_major_version)
+	{
+	    for $pg_minor_version ( "4", "3" )
+	    {
+		if ( -x "/Library/PostgreSQL/8." . $pg_minor_version . "/bin/psql" ) 
+		{
+		    $pg_major_version = 8; 
+		    $psql_exec = "/Library/PostgreSQL/8." . $pg_minor_version . "/bin";
+		    last; 
+		}
+	    }
+	}
+    }
+
+    if ( $psql_exec eq "" )
+    {
+	print STDERR "\nERROR: I haven't been able to find the psql command in your PATH!\n";
+	print STDERR "Please make sure PostgresQL is properly installed and try again.\n\n";
+
+	exit 1; 
+    }
+
+    
+
+    # 3c. CHECK POSTGRES VERSION: 
+
+    open (PSQLOUT, $psql_exec . "/psql --version|"); 
+
+    $psql_version_line = <PSQLOUT>; 
+    chop $psql_version_line; 
+    close PSQLOUT; 
+
+    my ($postgresName, $postgresNameLong, $postgresVersion) = split ( " ", $psql_version_line ); 
+
+    unless ( $postgresName eq "psql" && $postgresVersion =~ /^[0-9][0-9\.]*$/ )
+    {
+	print STDERR "\nERROR: Unexpected output from psql command!\n";
+	print STDERR "Please make sure PostgresQL is properly installed and try again.\n\n";
+
+	exit 1; 
+    }
+
+
+    my (@postgres_version_tokens) = split ( '\.', $postgresVersion ); 
+
+    unless ( ($postgres_version_tokens[0] == 8 && $postgres_version_tokens[1] >= 3) || ($postgres_version_tokens[0] >= 9) )
+    {
+	print STDERR "\nERROR: PostgresQL version 8.3, or newer, is required!\n";
+	print STDERR "Found a copy of psql ($psql_exec/psql) that belongs to version $postgresVersion.\n\n";
+	print STDERR "Please make sure the right version of PostgresQL is properly installed,\n";
+	print STDERR "and the right version of psql comes first in the PATH,\n";
+	print STDERR "then try again.\n";
+
+	exit 1; 
+    }
+
+    print "\n\nFound Postgres psql command, version $postgresVersion. Good.\n\n";
+
+    $pg_major_version = $postgres_version_tokens[0];
+    $pg_minor_version = $postgres_version_tokens[1];
+
+    # 4. CONFIGURE POSTGRES: 
+
+    print "\nConfiguring Postgres Database:\n";
+
+    
+
+    $< = $POSTGRES_SYS_UID; 
+    $> = $POSTGRES_SYS_UID; 
+
+    # 4a. CHECK IF POSTGRES IS RUNNING:
+    print "Checking if a local instance of Postgres is running and accessible...\n";
+
+    # (change to /tmp before executing the command below - 
+    # we are trying to do it as user postgres, and it may not have 
+    # access to the current, installer directory; the command would still 
+    # work, but there would be an error message from the shell init on screen 
+    # - potentially confusing)
+    chdir ("/tmp");
+
+    if (!system ($psql_exec . "/psql -c 'SELECT * FROM pg_roles' > /dev/null 2>&1"))
+    {
+	print "Yes, it is.\n";
+    }
+    else
+    {
+	print "Nope, I haven't been able to connect to the local instance of PostgresQL.\n";
+	print "daemon. Is postgresql running? \n";
+	print "On a RedHat system, you can check the status of the daemon with\n\n";
+	print "   service postgresql status\n\n";
+	print "and, if it's not running, start the daemon with\n\n";
+	print "   service postgresql start\n\n";
+	print "On MacOSX, use Applications -> PostgresQL -> Start Server.\n";
+	print "Also, please make sure that the daemon is listening to network connections,\n";
+	print "at leaset on the localhost interface. (See \"Installing Postgres\" section\n";
+	print "of the installation manual).\n";
+	print "Finally, please make sure that the postgres user can make localhost \n";
+	print "connections without supplying a password. (That's controlled by the \n";
+	print "\"localhost ... ident\" line in pg_hba.conf; again, please consult the \n";
+	print "installation manual).\n";
+
+
+	exit 1; 
+    }
+
+
+    # 4c. CHECK IF THIS DB ALREADY EXISTS:
+    
+    $psql_command_dbcheck = $psql_exec . "/psql -c \"\" -d " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . ">/dev/null 2>&1"; 
+    if ( ($exitcode = system($psql_command_dbcheck)) == 0 )
+    {
+	# switch back to root uid:
+	$> = 0; 
+	$< = 0; 
+	chdir ($cwd); 
+
+	print "WARNING! Database " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " already exists!\n";
+	print "\nPlease note that you can only use this installer to create a blank, \n"; 
+	print "new and shiny DVN database. I.e., you cannot install on top of an \n";
+	print "existing database. Please enter a different name for the DVN database.\n";
+	print "\nPress any key to continue, or ctrl-C to exit the installer...\n\n";
+
+	system "stty cbreak </dev/tty >/dev/tty 2>&1";
+	my $key = getc(STDIN);
+	system "stty -cbreak </dev/tty >/dev/tty 2>&1";
+	print "\n";
+
+	goto ENTERCONFIG; 
+ 
+    }
+
+    # 4d. CHECK IF THIS USER ALREADY EXISTS:
+
+    $psql_command_rolecheck = $psql_exec . "/psql -c \"\" -d postgres " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . " >/dev/null 2>&1";
+    if ( ($exitcode = system($psql_command_rolecheck)) == 0 )
+    {
+	print "User (role) . " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . " already exists;\n";
+	print "Proceeding.";
+    }
+    else 
+    {
+	# 4e. CREATE DVN DB USER:
+
+	print "\nCreating Postgres user (role) for the DVN:\n";
+
+	open TMPCMD, ">/tmp/pgcmd.$$.tmp";
+	
+	# with unencrypted password: 
+	#print TMPCMD "CREATE ROLE ".$CONFIG_DEFAULTS{'POSTGRES_USER'}." UNENCRYPTED PASSWORD '".$CONFIG_DEFAULTS{'POSTGRES_PASSWORD'}."' NOSUPERUSER CREATEDB CREATEROLE NOINHERIT LOGIN";
+	
+	# with md5-encrypted password:
+	$pg_password_md5 = &create_pg_hash ($CONFIG_DEFAULTS{'POSTGRES_USER'},$CONFIG_DEFAULTS{'POSTGRES_PASSWORD'}); 
+	my $sql_command = "CREATE ROLE \"".$CONFIG_DEFAULTS{'POSTGRES_USER'}."\" PASSWORD 'md5". $pg_password_md5 ."' NOSUPERUSER CREATEDB CREATEROLE INHERIT LOGIN";
+	
+	print TMPCMD $sql_command; 
+	close TMPCMD; 
+
+	my $psql_commandline = $psql_exec . "/psql -f /tmp/pgcmd.$$.tmp";
+	
+	unless ( ($exitcode = system($psql_commandline)) == 0 )
+	{
+	    print STDERR "Could not create the DVN Postgres user role!\n";
+	    print STDERR "(SQL: " . $sql_command . ")\n";
+	    print STDERR "(psql exit code: " . $exitcode . ")\n";
+	    exit 1; 
+	}
+
+	unlink "/tmp/pgcmd.$$.tmp";
+	print "done.\n";
+    }
+    
+    # 4f. CREATE DVN DB: 
+
+    print "\nCreating Postgres database:\n";
+
+    $psql_command = $psql_exec . "/createdb ".$CONFIG_DEFAULTS{'POSTGRES_DATABASE'}." --owner=".$CONFIG_DEFAULTS{'POSTGRES_USER'};
+
+    unless ( ($exitcode = system("$psql_command")) == 0 ) 
+    {
+	print STDERR "Could not create Postgres database for the DVN app!\n";
+	print STDERR "(command: " . $psql_command . ")\n";
+	print STDERR "(psql exit code: " . $exitcode . ")\n";
+	print STDERR "\naborting the installation (sorry!)\n\n";
+	exit 1; 
+    }
+
+
+# Changing back to root UID: 
+
+    $> = 0; 
+    $< = 0; 
+     
+    chdir ($cwd); 
+
+}
+else 
+{
+    if (0) # DEV. INSTALLER ONLY: 
+    {
+    print "\nIt is strongly recommended that you use a local PostgresQL server,\n";
+    print "running on localhost, in your development environment!\n\n";
+
+    print "Do you wish to continue?\n [y/n] ";
+
+
+    my $yesnocont = <>; chop $yesnocont;
+
+    while ( $yesnocont ne "y" && $yesnocont ne "n" )
+    {
+	print "Please enter 'y' or 'n'!\n";
+	print "(or ctrl-C to exit the installer)\n";
+	$yesnocont = <>; chop $yesnocont;
+    }
+
+    if ( $yesnocont eq "n" )
+    {
+	print "(aborting the installation)\n".
+	exit 0;
+    }
+    }
+
+    if ( $opts{$pg_only} )
+    {
+        print "The script must be run in the --pg_only mode ONLY locally,\n";
+        print "i.e., on the server where PostgresQL is running.\n";
+
+        exit 1; 
+    }
+    
+    print "In order to use a PostgresQL database running on a remote server,\n";
+    print "Please run this installer on that host with the \"--pg_only\" option:\n\n";
+    print "./install --pg_only\n\n";
+
+    print "Press any key to continue the installation process once that has been\n";
+    print "done. Or press ctrl-C to exit the installer.\n\n";
+
+    chdir ("/tmp");
+    system "stty cbreak </dev/tty >/dev/tty 2>&1";
+    my $key = getc(STDIN);
+    system "stty -cbreak </dev/tty >/dev/tty 2>&1";
+    print "\n";
+    chdir ($cwd);
+
+    # Check if the role and database have been created on the remote server:
+    # -- TODO; 
+
+    # Find out what Postgres version is running remotely:
+
+    $pg_major_version = 9;
+    $pg_minor_version = 1;
+
+    print "What version of PostgresQL is installed on the remote server?\n [" . $pg_major_version . "." . $pg_minor_version . "] ";
+
+
+    my $postgresVersion = <>; chop $postgresVersion;
+
+    while ( $postgresVersion ne "" && !($postgresVersion =~/^[0-9]+\.[0-9]+$/) )
+    {
+	print "Please enter valid Postgres version!\n";
+	print "(or ctrl-C to exit the installer)\n";
+	$postgresVersion = <>; chop $postgresVersion;
+    }
+
+    unless ( $postgresVersion eq "" )
+    {
+	my (@postgres_version_tokens) = split ( '\.', $postgresVersion ); 
+
+	unless ( ($postgres_version_tokens[0] == 8 && $postgres_version_tokens[1] >= 3) || ($postgres_version_tokens[0] >= 9) )
+	{
+	    print STDERR "\nERROR: PostgresQL version 8.3, or newer, is required!\n";
+	    print STDERR "Please make sure the right version of PostgresQL is properly installed\n";
+	    print STDERR "on the remote server, then try again.\n";
+	    
+	    exit 1; 
+	}
+
+	$pg_major_version = $postgres_version_tokens[0];
+	$pg_minor_version = $postgres_version_tokens[1];
+    }
+
+}
+
+
+if ( $postgresonly )
+{
+    print "\nOK, done.\n";
+    print "You can now resume the installation on the main DVN host.\n\n";
+    
+    exit 0; 
+}
+
+
+# 5. CONFIGURE GLASSFISH
+
+print "\nProceeding with the Glassfish setup.\n";
+print "\nChecking your Glassfish installation..."; 
+
+my $glassfish_dir = $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'}; 
+
+# 5a. CHECK IF GLASSFISH DIR LOOKS OK:
+
+print $glassfish_dir."/glassfish/domains/domain1";
+
+unless ( -d $glassfish_dir."/glassfish/domains/domain1" )
+{
+    # TODO: need better check than this
+
+    while ( ! ( -d $glassfish_dir."/glassfish/domains/domain1" ) )
+    {
+	print "\nInvalid Glassfish directory " . $glassfish_dir . "!\n";
+	print "Enter the root directory of your Glassfish installation:\n";
+	print "(Or ctrl-C to exit the installer): "; 
+
+	$glassfish_dir = <>; 
+	chop $glassfish_dir; 
+    }
+}
+
+print "OK!\n";
+
+# 5b. DETERMINE HOW MUCH MEMORY TO GIVE TO GLASSFISH AS HEAP:
+
+$gf_heap_default = "2048m"; 
+$sys_mem_total = 0; 
+
+if ( -e "/proc/meminfo" && open MEMINFO, "/proc/meminfo" ) 
+{
+    # Linux 
+
+    while ( $mline = <MEMINFO> )
+    {
+	if ( $mline =~ /MemTotal:[ \t]*([0-9]*) kB/ )
+	{
+	    $sys_mem_total = $1; 
+	}
+    }
+
+    close MEMINFO; 
+
+} 
+elsif ( -x "/usr/sbin/sysctl" ) 
+{
+    # MacOS X, probably...
+
+    $sys_mem_total = `/usr/sbin/sysctl -n hw.memsize`; 
+    chop $sys_mem_total;
+    if ($sys_mem_total > 0) 
+    {
+	$sys_mem_total = int ($sys_mem_total / 1024); 
+	# size in kb
+    }
+}
+
+if ( $sys_mem_total > 0 )
+{
+    # setting the default heap size limit to 3/8 of the available 
+    # amount of memory: 
+    $gf_heap_default = ( int ($sys_mem_total / (8 / 3 * 1024) ) ); 
+
+    print "\nSetting the heap limit for Glassfish to " . $gf_heap_default . "MB. \n"; 
+    print "You may need to adjust this setting to better suit \n";
+    print "your system.\n\n";
+
+    $gf_heap_default .= "m";
+
+}
+else 
+{
+    print "\nCould not determine the amount of memory on your system.\n";
+    print "Setting the heap limit for Glassfish to 2GB. You may need \n"; 
+    print "to  adjust the value to better suit your system.\n\n";
+}
+
+push @CONFIG_VARIABLES, "DEF_MEM_SIZE"; 
+$CONFIG_DEFAULTS{"DEF_MEM_SIZE"} = $gf_heap_default; 
+
+print "\nPress any key to continue...\n\n";
+
+system "stty cbreak </dev/tty >/dev/tty 2>&1";
+	my $key = getc(STDIN);
+	system "stty -cbreak </dev/tty >/dev/tty 2>&1";
+	print "\n";
+
+# 5c. GENERATE GLASSFISH CONFIGURATION FILE:
+
+print "\nWriting glassfish configuration file (domain.xml)... ";
+
+# 5cc. FIND THE "special-admin-indicator" IN THE ORIGINAL GLASSFISH CONFIG:
+
+open ( GFCNFG, $glassfish_dir."/glassfish/domains/domain1/config/domain.xml") || die $@; 
+
+while ( <GFCNFG> )
+{
+    if (/<secure-admin special-admin-indicator=\"([^\"]*)\"/)
+    {
+	$CONFIG_DEFAULTS{'GF_SPEC_INDICATOR'} = $1;
+    }
+}
+
+# (is it really a problem if we haven't found it?)
+
+close GFCNFG;
+
+open TEMPLATEIN, 'domain.xml.TEMPLATE'; 
+open CONFIGOUT, '>domain.xml';
+
+while( <TEMPLATEIN> )
+{
+    for $ENTRY (@CONFIG_VARIABLES)
+    {
+	$patin = '%' . $ENTRY . '%'; 
+	$patout = $CONFIG_DEFAULTS{$ENTRY}; 
+	
+	s/$patin/$patout/g;
+    }
+
+    print CONFIGOUT $_; 
+
+}
+
+close TEMPLATEIN; 
+close CONFIGOUT; 
+
+print "done.\n";
+
+system ("/bin/cp -f domain.xml ".$glassfish_dir."/glassfish/domains/domain1/config"); 
+#diagnostics needed!
+
+# check if the supllied config files are in the right place: 
+
+unless ( -f "config/logging.properties" )
+{
+    print "\nERROR! Configuration files not found in config dir!\n";
+    print "(are you running the installer in the right directory?\n";
+    print "Aborting...\n";
+    exit 1; 
+}
+
+print "\nCopying additional configuration files... ";
+
+system ( "/bin/cp -Rf config/* ".$glassfish_dir."/glassfish/domains/domain1/config"); 
+#diagnostics needed!
+
+# install pre-configured robots.txt blocking bot crawlers:
+system ( "/bin/cp -f robots.txt ".$glassfish_dir."/glassfish/domains/domain1/docroot"); 
+
+# install the DVN guides (HTML) into the application docroot: 
+system ( "/bin/cp -Rf doc/guides/* ".$glassfish_dir."/glassfish/domains/domain1/docroot/guides"); 
+
+
+print "done!\n";
+
+print "\nInstalling the Glassfish PostgresQL driver... ";
+
+my $install_driver_jar = "";
+
+if ( $pg_major_version == 8 ) 
+{
+    if ( $pg_minor_version == 3 ) 
+    {
+	$install_driver_jar = $POSTGRES_DRIVER_8_3;
+    }
+    elsif ( $pg_minor_version == 4 ) 
+    {
+	$install_driver_jar = $POSTGRES_DRIVER_8_4;
+    }
+}
+elsif ( $pg_major_version == 9 )
+{
+    if ( $pg_minor_version == 0 ) 
+    {
+	$install_driver_jar = $POSTGRES_DRIVER_9_0;
+    }
+    elsif ( $pg_minor_version == 1 ) 
+    {
+	$install_driver_jar = $POSTGRES_DRIVER_9_1;
+    }
+} 
+
+=poc
+unless ( $install_driver_jar ) 
+{
+    die "Installer could not find POSTGRES JDBC driver for your version of PostgresQL!\n";
+
+} 
+=cut
+
+system ( "/bin/cp", "pgdriver/" . $install_driver_jar, $glassfish_dir."/glassfish/lib"); 
+#diagnostics needed!
+
+print "done!\n";
+
+# 5d. STOP GLASSFISH (OK IF NOT RUNNING):
+print "\nStopping glassfish...\n";
+
+unless ( ($exit_code=system ($glassfish_dir."/bin/asadmin stop-domain domain1")) == 0 )
+{
+    print STDERR "(that's OK!)\n";
+}
+
+# 5dd. INSTALL PATCHED WEBCORE GLASSFISH MODULE: 
+
+$gf_webcore_jar = $glassfish_dir."/glassfish/modules/web-core.jar";
+
+system ("/bin/mv -f ".$gf_webcore_jar . " " . $gf_webcore_jar.".PRESERVED");
+system ("/bin/cp web-core.jar ".$gf_webcore_jar); 
+
+# 5ddd. DELETE EJB TIMER APP LOCK FILE, if exists (just in case!): 
+
+system ( "/bin/rm -f ".$glassfish_dir."/glassfish/domains/domain1/generated/ejb-timer-service-app" ); 
+
+# 5e. START GLASSFISH:
+print "\nStarting glassfish.\n";
+
+unless ( ($exit_code=system ($glassfish_dir."/bin/asadmin start-domain domain1")) == 0 )
+{
+	print STDERR "Could not start glassfish!\n";
+	print STDERR "(exit code: " . $exitcode . ")\n";
+	exit 1; 
+}
+
+
+# check if glassfish is running: 
+# TODO. 
+
+# 6. DEPLOY APPLICATION:
+# 6a. DO WE HAVE ANT? 
+#  (we are no longer using ant to deply -- L.A.)
+#
+#$sys_path = $ENV{'PATH'}; 
+#@sys_path_dirs = split ( ":", $sys_path ); 
+
+#$ant_exec = ""; 
+#
+#for $sys_path_dir ( @sys_path_dirs )
+#{
+#    if ( -x $sys_path_dir . "/ant" ) 
+#    {
+#	$ant_exec = $sys_path_dir . "/ant"; 
+#	last; 
+#    }
+#}
+#
+#if ( $ant_exec eq "" )
+#{
+#    print STDERR "\nERROR: I haven't been able to find ant command in your PATH!\n";
+#    print STDERR "Please make sure and is installed and in your PATH; then try again.\n\n";
+#
+#    exit 1; 
+#}
+# 6b. TRY TO DEPLOY:
+
+print "\nAttempting to deploy the application:\n\n";
+
+$CONFIG_DEFAULTS{'GLASSFISH_ADMIN_PASSWORD'} = 'adminadmin'; 
+# TODO: ask for password! -- in case they have already changed it
+# (update: chances are we don't even need the password anymore, as 
+# long as we are deploying locally (?))
+
+my $glassfish_password = $CONFIG_DEFAULTS{'GLASSFISH_ADMIN_PASSWORD'}; 
+
+# create deployment properties files:
+#   (these properties files are no longer used, because we are no longer
+#   using ant to deploy the app. -- L.A.)
+
+#for $prop_file ('AS', 'glassfish') 
+#{
+#    open ( TEMPLIN, "appdeploy/" . $prop_file . ".properties.TEMPLATE" ) 
+#	|| die "failed to open appdeploy/" . $prop_file . ".properties.TEMPLATE";
+#    open ( PROPOUT, ">appdeploy/" . $prop_file . ".properties" ) 
+#	|| die "failed to open appdeploy/" . $prop_file . ".properties for writing";
+#
+#    while( <TEMPLIN> )
+#    {
+#	s/%GF_ADMIN_PASSWORD%/$glassfish_password/g;
+#	s/%GF_ROOT_DIR%/$glassfish_dir/g;
+#	print PROPOUT $_; 
+#    }
+#
+#    close TEMPLIN; 
+#    close PROPOUT; 
+#}
+
+# Create the .asadminpass file, or replace it, if exists:
+
+$asadminpass_file = $ENV{'HOME'} . "/.asadminpass";
+
+if ( -e $asadminpass_file )
+{
+    system ("/bin/mv -f " . $asadminpass_file . " " . $asadminpass_file . ".PRESERVED");
+}
+
+system ("echo 'asadmin://admin@localhost:4848 ' > " . $asadminpass_file); 
+
+$deploy_command = $glassfish_dir."/bin/asadmin deploy --force=true --name=DVN-web dist/DVN-web.war";
+
+unless ( ($exit_code = system ("cd appdeploy; " . $deploy_command)) == 0 )
+{
+	print STDERR "Could not deploy DVN application!\n";
+	print STDERR "(exit code: " . $exitcode . ")\n";
+	exit 1; 
+}
+
+if ( $pg_local_connection )
+{
+    print "\nOK; now we are going to stop glassfish and populate the database with\n";
+    print "some initial content, then start glassfish again.\n";
+}
+else
+{
+    print "\nOK; stopping glasfish.\n";
+}
+
+
+# 6c. SHUT DOWN:
+
+$gf_stop_command = $glassfish_dir."/bin/asadmin stop-domain domain1"; 
+
+unless ( ($exit_code = system ($gf_stop_command)) == 0 )
+{
+	print STDERR "Could not stop glassfish!\n";
+	print STDERR "(command line: " . $gf_stop_command . ")\n";
+	print STDERR "(exit code: " . $exitcode . ")\n";
+	print STDERR "\nPlease finish the installation process manually: \n";
+	print STDERR "stop/kill glassfish; then populate the database with \n";
+	print STDERR "the supplied initial content, by executing the following \n";
+	print STDERR "command, *as Unix user postgres*: \n\n";
+
+	$psql_command = $psql_exec . "/psql -d $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} -f " . $SQL_REFERENCE_DATA;
+
+	print STDERR $psql_command . "\n\n";
+	print STDERR "Then start glassfish again... Voila, you should then have \n";
+	print STDERR "a running DVN instance at the following URL:\n\n";
+	print STDERR "  http://" . $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} . "/dvn\n";
+
+	print STDERR "\naborting the installer... (sorry!)\n";
+
+	exit 1; 
+}
+
+# 7. POPULATE DATABASE:
+
+if ( $pg_local_connection )
+{
+    # 7a. POPULATE LOCALLY:
+    print "\nPopulating the database (local PostgresQL instance):\n\n";
+
+    # Copy the SQL file to /tmp, where user postgres will definitely 
+    # have read access to it: 
+
+    copy("referenceData.sql","/tmp") or die "Could not copy referenceData.sql to /tmp: $!";
+
+    $< = $POSTGRES_SYS_UID; 
+    $> = $POSTGRES_SYS_UID; 
+    chdir ("/tmp"); 
+    $psql_command = $psql_exec . "/psql -d $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} -f referenceData.sql";
+
+    unless ( ($exitcode = system("$psql_command")) == 0 ) 
+    {
+	print STDERR "Could not populate Postgres database for the DVN app!\n";
+	print STDERR "(command: " . $psql_command . ")\n";
+	print STDERR "(psql exit code: " . $exitcode . ")\n";
+	print STDERR "\nYou must populate the database before you can use your new\n";
+	print STDERR "DVN instance. Please consult the installation manual and/or\n";
+	print STDERR "seek support from the DVN team.\n\n";
+	exit 1; 
+	
+    }
+
+    chdir ($cwd); 
+    print "\nOK, done!\n";
+
+}
+else 
+{
+    # 7b. INSTRUCT THE USER TO POPULATE THE DB ON THE REMOTE SERVER:
+    # NOT SUPPORTED YET -- TODO
+    print "The database needs to be populated with some intial content \n"; 
+    print "before we restart the DVN one last time. \n";
+    print "However, populating a database on a remote PostgresQL server "; 
+    print "is not supported yet!\n";
+    print "Please copy the file referenceData.sql (found in this directory)\n";
+    print "onto the remote server and populate the database manually,\n";
+    print "as user postgres, with the following command:\n\n";
+    print "   psql -d $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} -f referenceData.sql\n";
+    print "then start glassfish again on this server with \n\n";
+    print "   " . $glassfish_dir."/bin/asadmin start-domain domain1\n\n";
+
+    $> = 0; 
+    $< = 0; 
+
+    exit 0; 
+    
+}
+
+# back to root:
+
+$> = 0; 
+$< = 0; 
+
+# 8. START GLASSFISH AGAIN:
+print "\nStarting glassfish, again:\n\n";
+
+$gf_start_command = $glassfish_dir."/bin/asadmin start-domain domain1"; 
+
+# delete the EJB TIMER app lock file, if exists (just in case!): 
+system ( "/bin/rm -f ".$glassfish_dir."/glassfish/domains/domain1/generated/ejb-timer-service-app" ); 
+
+unless ( ($exit_code = system ($gf_start_command)) == 0 )
+{
+	print STDERR "Could not start glassfish!\n";
+	print STDERR "(command line: " . $gf_start_command . ")\n";
+	print STDERR "(exit code: " . $exit_code . ")\n";
+	exit 1; 
+}
+
+
+print "\nYou should now have a running DVN instance;\n";
+print "Please go to the application at the following URL:\n\n";
+print "  http://" . $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} . "/dvn\n";
+print "\nand log in by using \"networkAdmin\" as both the user name\n";
+print "and password. Click the \"networkAdmin\" link on the right side\n";
+print "Of the main screen, then click \"Update Account\". Change this\n";
+print "default password and default e-mail address.\n";
+
+# 9. FINALLY, CHECK IF RSERVE IS RUNNING: 
+print "\n\nFinally, checking if Rserve is running and accessible...\n";
+
+unless ( $CONFIG_DEFAULTS{'RSERVE_PORT'}=~/^[0-9][0-9]*$/ )
+{
+    print $CONFIG_DEFAULTS{'RSERVE_HOST'} . " does not look like a valid port number,\n";
+    print "defaulting to 6311.\n\n";
+
+    $CONFIG_DEFAULTS{'RSERVE_PORT'} = 6311; 
+}
+    
+my ( $rserve_iaddr, $rserve_paddr, $rserve_proto );
+
+unless ( $rserve_iaddr = inet_aton($CONFIG_DEFAULTS{'RSERVE_HOST'}) )
+{
+    print STDERR "Could not look up $CONFIG_DEFAULTS{'RSERVE_HOST'},\n";
+    print STDERR "the host you specified as your R server.\n";
+    print STDERR "\nDVN can function without a working R server, but\n";
+    print STDERR "much of the functionality concerning running statistics\n";
+    print STDERR "and analysis on quantitative data will not be available.\n";
+    print STDERR "Please consult the Installers guide for more info.\n";
+
+    exit 0;
+}
+
+$rserve_paddr = sockaddr_in($CONFIG_DEFAULTS{'RSERVE_PORT'}, $rserve_iaddr);
+$rserve_proto = getprotobyname('tcp');
+
+unless ( socket(SOCK, PF_INET, SOCK_STREAM, $rserve_proto) &&
+	connect(SOCK, $rserve_paddr) ) 
+{
+    print STDERR "Could not establish connection to $CONFIG_DEFAULTS{'RSERVE_HOST'}\n";
+    print STDERR "on port $CONFIG_DEFAULTS{'RSERVE_PORT'}, the address you provided\n";
+    print STDERR "for your R server.\n";
+    print STDERR "DVN can function without a working R server, but\n";
+    print STDERR "much of the functionality concerning running statistics\n";
+    print STDERR "and analysis on quantitative data will not be available.\n";
+    print STDERR "Please consult the \"Installing R\" section in the Installers guide\n";
+    print STDERR "for more info.\n";
+
+    exit 0;
+    
+}
+
+close (SOCK); 
+print "\nOK!\n";
+
+exit 0; 
+
+
+sub create_pg_hash {
+    local $pg_username = shift @_; 
+    local $pg_password = shift @_; 
+
+    $encode_line = $pg_password . $pg_username; 
+
+    # for Redhat: 
+
+    ##print STDERR "executing /bin/echo -n $encode_line | md5sum\n"; 
+
+    if ( $WORKING_OS eq "MacOSX" )
+    {
+	$hash = `/bin/echo -n $encode_line | md5`; 
+    }
+    else 
+    {
+	$hash = `/bin/echo -n $encode_line | md5sum`; 
+    }
+
+    chop $hash; 
+
+    $hash =~s/  \-$//; 
+
+    if ( (length($hash) != 32) || ($hash !~ /^[0-9a-f]*$/) ) 
+    {
+	print STDERR "Failed to generate a MD5-encrypted password hash for the Postgres database.\n";
+	exit 1; 
+    }
+
+
+    return $hash;
+}