package RSAT::server;

require RSAT::util;
require RSAT::message;
require RSAT::error;
# use MIME::Lite;

################################################################
## Check that the environment variable RSAT has been defined
unless ($ENV{RSAT}) {
    $ENV{RSAT} = $0; #
#    $ENV{RSAT} =~ s|\/[^\/]+$||g; ## Guess RSAT path from module full name
    $ENV{RSAT} =~ s|/*perl-scripts.*||; ## Guess RSAT path from module full name
    $ENV{RSAT} =~ s|/*public_html.*||; ## Guess RSAT path from module full name
    if ($ENV{RSAT} eq "") {
	$ENV{RSAT} = `pwd`;
	chomp $ENV{RSAT};
    }
}

## test Morgane (feb 2015) => does not seem to work...
$ENV{PYTHONPATH}=$ENV{RSAT}."/lib/python2.7/site-packages";

################################################################
## Get the version of the code (last modification of git)
## to be displayed on the web servers.
##
## There is no real "version" in git, so one way is to get
## the time of the last commit
## commit 7336dc8063ae5c98e4857dd8b094cb42e5f70835
## Merge: 7f4f1fb 3c768b0
## Author: amedina <medina.alexiel@gmail.com>
## Date:   Wed Feb 11 23:47:48 2015 -0500

sub GetGitLastCommitDate {
    my $version_git = `git log | head -n 4 | grep Date` ;
    $version_git =~ s/Date://;
    $version_git =~ s/^\s*\w+\s+//;
    $version_git =~ s/\D+\w+\s*$//;
    &RSAT::message::Info("&RSAT::server::GetGitLastCommitDate()", "log version", $version_git)
	if ($main::verbose >= 5);
    return $version_git;
}

################################################################
=pod

=item GetProgramPath

Return the path of a program.

The function successively checks if the program exists in various
directories: 

1) $ENV{RSAT_BIN} (defined in RSAT_config.props)
2) $ENV{RSAT}/bin
3) In the subcommands supported by the rsat command
4) In the perl-scripts and python-scripts subdirectories of RSAT 
5) Anywhere in the user path

Usage:
    my $program_path = &RSAT::server::GetProgramPath("program_name", $die_on_error, @preferred_paths);

=cut

sub GetProgramPath {
  my ($program_name, $die_on_error, @preferred_paths) = @_;
  my $program_path = "";
  
  ## Find the preferred location of the program
  my @rsat_path = @preferred_paths;
  if (defined($ENV{RSAT_BIN})) {
    push @rsat_path, ($ENV{RSAT_BIN});
  };
  
  ## If the RSAT path contains the searcher program, use this
  ## version as preferred path.
  push @rsat_path, ($ENV{RSAT}."/bin",
		    $ENV{RSAT}."/python-scripts",
		    $ENV{RSAT}."/perl-scripts",
		    ".");
  
  my $path_found = 0;
  foreach my $dir (@rsat_path) {
      my $possible_path = $dir."/".$program_name;
      $possible_path =~ s|/+|/|g;
      #      &RSAT::message::Debug("GetProgramPath()", "testing", $program_name, $possible_path) if ($main::verbose >= 10);
      if (-e $possible_path) {
	  $program_path = $possible_path;
	  last;
      }
  }

  ## Test if the command is known as rsat subcommand
  my @subcommands = `rsat --list`;
  my %rsat_cmd = ();
  foreach my $cmd (@subcommands) {
      $cmd = &RSAT::util::trim($cmd);
      $rsat_cmd{$cmd} = $cmd;
      $rsat_cmd_lc{lc($cmd)} = $cmd;
  }
  my @rsat_cmd = sort(keys(%rsat_cmd));
  my @rsat_cmd_lc = sort(keys(%rsat_cmd_lc));
  if (defined($rsat_cmd{$program_name})) {
#      &RSAT::message::Debug("GetProgramPath()", "rsat subcommand", "rsat ".$program_name) if ($main::verbose >= 5);
      return("rsat ".$program_name);
  }
  
  #   die "rsat subcommands:\n\t", join("\n\t", @rsat_cmd), "\n";
  
  ## If the path has not ben found yet, find the program anywhere in
  ## the user path
  unless ($program_path) {
      $program_path = `which $program_name`;
      chomp($program_path);
  }

  ## Check if the program path has been found
  unless ($program_path) {
    if ($die_on_error) {
      &RSAT::error::FatalError("The program ".$program_name." is not found in your path.");
    } else {
      &RSAT::message::Warning("The program ".$program_name." is not found in your path.");
      return();
    }
  }

  ## Check if the program can be executed
  unless (-x $program_path) {
    if ($die_on_error) {
      &RSAT::error::FatalError("The program ".$program_path." cannot be run. ");
    } else {
      &RSAT::message::Warning("The program ".$program_path." cannot be run. ");
    }
  }

  &RSAT::message::Info("&RSAT::server::GetProgramPath()", "path found", $program_path)
      if ($main::verbose >= 4);
  return $program_path;
}

################################################################
#### increment the counter file for monitoring web access
sub UpdateCounterFile {
  my $nb_visitors = 1;

  ### read previous counter value
  if (-e $counter_file) {
    open(COUNTER, "<$counter_file");
    #flock(COUNTER, 2);
    $nb_visitors = <COUNTER>;
    #flock(COUNTER,8);
    close(COUNTER);
    $nb_visitors++;
  }

  ### save new counter value
  open(COUNTER, ">$counter_file");
  #flock(COUNTER,2);
  print COUNTER $nb_visitors;
  #flock(COUNTER,8);
  close(COUNTER);
  return $nb_visitors;
}


=pod

=item B<DetectDeniedIP()>

Check that the client IP address is not blacklisted on this RSAT
server. If denied, die with error message.

=cut

sub DetectDeniedIP {

    ## IP address of the client computer
    my $client_ip = &RSAT::util::trim($ENV{'REMOTE_ADDR'});
    &RSAT::message::Info("Your IP address: '".$client_ip."'") if ($main::verbose >= 10);

    ## File with the list of denied addresses
    my $rsat_site = $ENV{rsat_site};
    my ($sec, $min, $hour,$day,$month,$year) = localtime(time());
    $year += 1900;

    ## The authorized IP file contains manually entered addresses that are
    ## corrections for erroneous denial. If the client IP appears in this
    ## list, no need to check denied addresses.
    my $authorized_ip_file= $ENV{RSAT}."/authorized_IP_addresses_".$rsat_site."_".$year.".tab";
    if (-e $authorized_ip_file) {
      my ($in) = &RSAT::util::OpenInputFile($authorized_ip_file);
      while (<$in>) {
	chomp();
	next unless /\S/; ## Skip empty lines
	next if /^;/; ## Skip comment lines
	next if /^#/; ## Skip comment lines
	my ($ip, $nb, $reason) = split(/\s+/, $_);
	if ($client_ip eq $ip) {
	    &RSAT::message::Info("Welcome", $client_ip) if ($ENV{rsat_echo} >= 3);
	    return (0);	
	}
      }
    }    

    ## Read the file of denied IP addresses
    my $denied_ip_file= $ENV{RSAT}."/denied_IP_addresses_".$rsat_site."_".$year.".tab";
    &RSAT::message::Info("Denied IP file", &RSAT::util::hide_RSAT_path($denied_ip_file)) if ($main::verbose >= 5);

    if (-e $denied_ip_file) {
      my ($in) = &RSAT::util::OpenInputFile($denied_ip_file);
      while (<$in>) {
	chomp();
	next unless /\S/; ## Skip empty lines
	next if /^;/; ## Skip comment lines
	next if /^#/; ## Skip comment lines
	my ($ip, $nb, $reason) = split(/\s+/, $_);
	&RSAT::message::Debug("Denied '".$ip."'",
			      "Your IP address: '".$client_ip."'") if ($main::verbose >= 10);

	if ($client_ip eq $ip) {
	  ################################################################
	  ## Report denied access

	  ## Check script name
	  my $script_name = &RSAT::util::ShortFileName($0);

	  ## Update web attacks denial file
	  my $denial_file = $main::denied_access_log_file;
	  if (open DENIAL, ">>".$denial_file) {
	    my $date = &RSAT::util::AlphaDate();
	    print DENIAL join ("\t",
			       $date,
			       $ENV{rsat_site},
			       $ENV{'REMOTE_ADDR'},
			       $script_name,
			       $user_email,
			       $reason,
			      ), "\n";
	    close DENIAL;
	  }
	  chmod 0777, $denial_file;

	  ## Issue denial message and die
	  &RSAT::error::FatalError("Access denied: your IP address (".$client_ip.") has been blacklisted on this server.", 
				   "Reason: ".$reason,
				   "If you are a real user of the tools, please contact the system administrator: ".$ENV{rsat_server_admin});
	}
      }
    }
    return (0);
}




################################################################
### store info into a log file in a conveninent way for 
### subsequent login statistics
### Usage:
###     &UpdateLogFile($script_name, $message, $log_file, $user_email);
sub UpdateLogFile {
  my ($script_name, $message, $log_file, $user_email) = @_;

  ## Check script name
  unless ($script_name) {
    $script_name = &RSAT::util::ShortFileName($0);
  }

  ## Check log file
  unless ($log_file) {
    if ($main::log_file) {
      $log_file = $main::log_file;
    } else {
      &RSAT::message::Warning("&RSAT::server::UpdateLogFile() called without \$log_file argument") if ($main::verbose >= 4);
      return;
    }
  }

  &RSAT::message::Debug("&RSAT::server::UpdateLogFile()",
			"<p>script=".$script_name,
			"<p>message=".$message,
			"<p>log=".$log_file,
			"<p>email=".$user_email,
			 ) if ($main::verbose >= 5);


  if (open LOG, ">>".$log_file) {
    #flock(LOG,2);
    $date = &RSAT::util::AlphaDate();
    $date =~ s/\n//;
    print LOG join ("\t",
		    $date,
		    $ENV{rsat_site},
		    $ENV{'REMOTE_ADDR'},
		    $script_name,
		    $user_email,
		    $message
		    ), "\n";
    #flock(LOG,8);
    close LOG;
  }
  chmod 0777, $log_file;
}


################################################################
## Report a suspicious content in a Web form, considered as potential
## Web attack.
##
### Usage:
###     &ReportWebAttack($script_name, $message, $log_file, $user_email);
sub ReportWebAttack {
  my ($script_name, $attack_type, $attack_detail, $user_email) = @_;

  ## Check script name
  unless ($script_name) {
    $script_name = &RSAT::util::ShortFileName($0);
  }

  ## Update web attacks log file
  $log_file = $main::web_attacks_log_file;
  if (open LOG, ">>".$log_file) {
    #flock(LOG,2);
    $date = &RSAT::util::AlphaDate();
    $date =~ s/\n//;
    print LOG join ("\t",
		    $date,
		    $ENV{rsat_site},
		    $ENV{'REMOTE_ADDR'},
		    $script_name,
		    $user_email,
		    $attack_type,
		    $attack_detail,
		    ), "\n";
    #flock(LOG,8);
    close LOG;
  }
  chmod 0777, $log_file;

  &RSAT::message::Debug("&RSAT::server::ReportWebAttack()",
			"<p>script=".$script_name,
			"<p>message=".$message,
			"<p>log=".$log_file,
			"<p>email=".$user_email,
			 ) if ($main::verbose >= 5);

}


################################################################
## Append the execution time of a the current script in a specific log file
## Usage:
##     &UpdateExecTimeLogFile($start_time, $done_time, $elapsed);
sub UpdateExecTimeLogFile {
  my ($start_time, $done_time, $elapsed, $warn_message) = @_;

  my $script_name = &RSAT::util::ShortFileName($0) || 'undefined';
  my $command = join (" ", $script_name, @ARGV);

  ## Assign value to uninitialized values
  unless ($start_time) {
    $start_time = "Unspecified";
  }
  unless ($done_time) {
    $done_time = "Unspecified";
  }
  unless ($start_time) {
    $elapsed = "Unspecified";
  }
  my $login = getlogin || getpwuid($<) || "Kilroy";

  ## Get host name
  my $hostname = `hostname`;
  chomp($hostname);

  ## Get remote address (only for Web queries)
  my $remote_addr = "";
  if (defined($ENV{REMOTE_ADDR})) {
    $remote_addr = $ENV{REMOTE_ADDR};
  }

  &RSAT::message::TimeWarn("Updating execution time log file", $main::exec_time_log_file)
    if ($main::verbose >= 4);

  ## Write header of the exec time log file if required
  &RSAT::message::Debug("exec_time_log_file", $main::exec_time_log_file) if ($main::verbose >= 5);
  unless (-e $main::exec_time_log_file) {
    &RSAT::message::Info("Creating execution time log file",  $main::exec_time_log_file) if ($main::verbose >= 2);
    open LOG, ">".$main::exec_time_log_file;
    print LOG join ("\t",
		    "#start_date.time",
		    "done_date.time  ",
		    "seconds",
		    "PID",
		    "hostname",
		    "username",
		    "script_name",
		    "command",
		    "remote_addr",
		   ), "\n";
    close LOG;
  }

  open LOG, ">>".$main::exec_time_log_file;
  print LOG join ("\t",
		  $start_time,
		  $done_time,
		  $elapsed,
		  $hostname,
		  $$,
		  $login,
		  $script_name,
		  $command,
		  $remote_addr,
		 ), "\n";
  close LOG;
  chmod 0777, $main::exec_time_log_file;
}



################################################################
#### send a unix command to remove a file the next day
#### Usage:
#### &DelayedRemoval($file_to_remove, $delay);
####
sub DelayedRemoval {
    my ($file_to_remove, $delay, $check_file) = @_;
    $delay = $delay || "24 hours";

    #### THIS FUNCTION IS TEMPORARILY INACTIVATED BECAUSE IT MOBILIZES
    #### A LOT OF MEMORY
    return();

    if ($check_file) {
      unless (-e $file_to_remove) {
	&MessageToAdmin("DelayedRemoval: file $file_to_remove does not exist");
	return();
      }
      unless (-r $file_to_remove) {
	&MessageToAdmin("DelayedRemoval: file $file_to_remove is not readable");
	return();
    }
      unless (-w $file_to_remove) {
	&MessageToAdmin("DelayedRemoval: file $file_to_remove is not writable");
	return();
      }
    }
    &MessageToAdmin("DelayedRemoval: file $file_to_remove will be removed in $delay") 
	if ($ENV{rsat_echo} >= 2);

    open REMOVE, "| at now + $delay";
    print REMOVE "rm -f $file_to_remove \n";
    close REMOVE;
}


################################################################
## Read props file
sub ReadProperties {
  if ($0 =~ /([^(\/)]+)$/) {
    ## This flag is activated if the site-specific config is not found
    my $default_props = 0;

    ## Identify the property file
    my $property_file = "";
    if (defined($ENV{RSAT})) {
      $property_file = "$ENV{RSAT}/RSAT_config.props";
    } else {
      $property_file = $`."../RSAT_config.props"; #`
    }

    ## Check that site-specific property file has been created (nd
    ## hopefully configured). If not, issue warning and try to
    ## improvise with the default config file distributed with RSAT
    ## (no guarantee).
    unless (-e $property_file) {
      &RSAT::message::Warning("This RSAT site is not properly configured.\n",
			      '$ENV{RSAT}='.$ENV{RSAT},
			      "\n\tProperty file does not exist: ".$property_file,
			      "\n\tPlease contact the system administrator ".$ENV{SERVER_ADMIN});
      $property_file = $`."../RSAT_config_default.props"; #`
      $default_props = 1;
    }

    ## Load RSAT site-specific properties
    if (-e $property_file) {
      &RSAT::message::Info("Reading property file", $property_file) if ($main::verbose >= 5);
      my ($props) = &RSAT::util::OpenInputFile($property_file);
      while (<$props>) {
	next if (/^#/);
	next if (/^;/);
	next unless (/\S/);
	chomp();
	if (/\=/) {
	  my $value = $'; #'
	  my $key = $`; #`
#	  if ($default_props) {
	  $value =~ s|\[RSAT_PARENT_PATH\]/rsat|$ENV{RSAT}|g;
#	  }
	  $ENV{$key} = $value;
	  $server::config{$key} = $value;
#	  &RSAT::message::Info("Site property", sprintf("%-15s\t%s", $key, $ENV{$key})) if ($main::verbose >= 10);
	}
      }
    }
  }
}


################################################################
## Read Perl config files.
##
##  WARNING: This was the old way to treat the configuration. The config is
## now read from the propery file RSAT_config.props. This piece of code should
## be supopressed but I firts have to check that everything works fine.
sub ReadConfig {
  if ($0 =~ /([^(\/)]+)$/) {
    my $config_file;
    if (-e $`."../RSA.config") {
      $config_file = $`."../RSA.config";
    } elsif (-e $`."../../RSA.config") {
      $config_file = $`."../../RSA.config";
    }
    &RSAT::message::Info("RSAT config file", $config_file) if ($main::verbose >= 4);
    if ($config_file) {
      require $config_file;
    } else {
      return();
      &RSAT::error::FatalError("Cannot find the old-format config file", "RSA.config", "from dir", $`);
    }

    ## Read user-defined local configuration if defined
    if ($ENV{'RSA_LOCAL_CONFIG'}) {
      if (-e $ENV{'RSA_LOCAL_CONFIG'}) {
	&RSAT::message::Info("Reading local configuration file", $ENV{'RSA_LOCAL_CONFIG'}) if ($main::verbose >= 1);
	if (-r $ENV{'RSA_LOCAL_CONFIG'}) {
	  require $ENV{'RSA_LOCAL_CONFIG'};
	} else {
	  warn (";WARNING: cannot read local config file ",
		$ENV{'RSA_LOCAL_CONFIG'},
		"\n"),
	      }
      } else {
	warn (";WARNING: local config file ",
	      $ENV{'RSA_LOCAL_CONFIG'},
	      " does not exist\n"),
	    }
    }
  } else {
    &RSAT::error::FatalError("Error: problem when opening config file. Please contact Jacques.van-Helden\@univ-amu.fr");
  }
}


################################################################
## Load additional genomes, locally installed in user's account
sub LoadLocalOrganisms {
  ## TO BE IMPLEMENTED
  ## - load the organisms from a tab-delimited file
  ## - check that the organisms ar esuppored by get-orthologs

  if ($ENV{'RSAT_LOCAL_ORGANISMS'}) {
    if (-e $ENV{'RSAT_LOCAL_ORGANISMS'}) {
      if (-r $ENV{'RSAT_LOCAL_ORGANISMS'}) {
	&RSAT::message::Warning("LOADING OF LOCAL ORGANISMS STILL HAS TO BE IMPLEMENTED. IGNORED.");
      } else {
	&RSAT::message::Warning(";WARNING: cannot read local config file ", $ENV{'RSAT_LOCAL_ORGANISMS'})
      }
    } else {
      &RSAT::message::Warning(";WARNING: local config file does not exist ", $ENV{'RSAT_LOCAL_ORGANISMS'})
    }
  }
}

################################################################
## Initialize the global variables required for RSAT
## MANY OF THESE VARIABLES ARE OBSOLETE
## THIS SHOULD BE CLEANED WHEN I FIND TIME TO DO IT
sub InitRSAT {
  umask 0022;
  
#  $ENV{RSA_OUTPUT_CONTEXT} = "screen";

  &ReadProperties();

  ## Load the list of user-specific supported organisms
  &LoadLocalOrganisms();


  ## Make sure that the variable RSAT_WWW is defined
  if ((!defined($ENV{rsat_www})) || ($ENV{rsat_www} eq "auto")) {
    # use Sys::Hostname;
    # use Socket;
    # my($addr)=inet_ntoa((gethostbyname(hostname))[4]);
    # my $hostname = hostname();
    # my @addresses = inet_ntoa((gethostbyname($hostname))[4]); ## In principle te function gethostbyname() should return all the IP addresses, but it seems to return only one

#    use Net::Address::IP::Local;
#    my @addresses = Net::Address::IP::Local->public;
#    my $ip_address = $addresses[0];

    my $ip_address = $ENV{HTTP_HOST} || "localhost";

    &RSAT::message::Debug("Host IP addresses", scalar(@addresses), "\n", join ("\n", '@addresses', @addresses)) if ($main::verbose >= 4);
    $ENV{rsat_www} = "http://".$ip_address."/rsat/";
    $ENV{rsat_ws} = "http://".$ip_address."/rsat/";
    &RSAT::message::Debug("RSAT_WWW", $ENV{rsat_www}) if ($main::verbose >= 4);
  }

  ## Directories
  $main::BIN = "$ENV{RSAT}/bin";
  $main::LIB = "$ENV{RSAT}/ext_lib";

  ################################################################
  ## !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  ## JvH, 2014-02-19 : I suppress this, because with the user-specific
  ## temp folders, all users should not have the possibility to create
  ## a directory in the public_html folder anymore

  ## Check temporary directory
#  $main::TMP = $ENV{RSAT}."/public_html/tmp";
#  &RSAT::util::CheckOutDir($main::TMP);
#  chmod(0777, $main::TMP);
#   &RSAT::message::Debug("Temporary dir", $main::TMP) if ($main::verbose >= 5);

  ## !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  ################################################################
  $main::SCRIPTS = $ENV{RSAT}."/perl-scripts";
  $main::PYTHON = $ENV{RSAT}."/python-scripts";
  $main::C_SCRIPTS = $ENV{RSAT}."/bin";

  ################################################################
  ## Redirect queries to a remote server
  ##
  ## This piece of code used to ensure load balancing between several
  ## machines, but it relies on rsh, which is not a safe protocol. In
  ## case of need, it could be adapted to work with ssh in the
  ## future. Anyway, this will probably be replaced by more efficient
  ## protocols for grid computation.
  if ($main::REMOTE_SERVER) {
    my $login = getlogin();
    if (($login eq "webserv") || !($login)) {
      $main::NICE = "nice +5";
      $main::RSH = "rsh -l jvanheld ${REMOTE_SERVER} $NICE";
      $main::SCRIPTS = "$RSH rsa-tools/perl-scripts";
      $main::BIN = "$RSH rsa-tools/bin";
    }
  }
  $main::HTML = "$ENV{RSAT}/public_html"; 
  $main::WWW_TMP = "$ENV{rsat_www}/tmp";
  $main::LOGS = "$ENV{RSAT}/logs";
  $main::counter_file = $main::LOGS."/count-file";
  my ($sec, $min, $hour,$day,$month,$year) = localtime(time);
  $main::log_file = join("", $main::LOGS, "/log-file_", $ENV{rsat_site}, sprintf("_%04d_%02d", $year+1900,$month+1));
  $main::web_attacks_log_file = join("", $main::LOGS, "/web_attacks_log_", $ENV{rsat_site}, sprintf("_%04d_%02d", $year+1900,$month+1), ".txt");
  $main::denied_access_log_file = join("", $main::LOGS, "/denied_access_log_", $ENV{rsat_site}, sprintf("_%04d_%02d", $year+1900,$month+1), ".txt");
  $main::exec_time_log_file = join("", $main::LOGS, "/exec_time_log_", $ENV{rsat_site}, sprintf("_%04d_%02d", $year+1900,$month+1), ".txt");
  $main::start_time_log_file = join("", $main::LOGS, "/start_time_log_", $ENV{rsat_site}, sprintf("_%04d_%02d", $year+1900,$month+1), ".txt");
  $main::date = &RSAT::util::AlphaDate();
}


=pod

=item supported_motif_databases()

Returns a hash table with the specification of motif databases on the
current RSAT instance.

Note: the keys of the hash table can be queriedd in a case-insensitive
way by using lowercases (keys are both in the native case and in
lowercases).

Usage: 
 my %matrix_db = &RSAT::server::supported_motif_databases();

=cut
sub supported_motif_databases {
  our %matrix_db = ();
  
  ## Load the file containing the path to the databases
  my $mat_db = $ENV{RSAT}."/public_html/motif_databases/db_matrix_files.tab" ;
  unless (-e $mat_db) {
    &RSAT::message::Warning( "Motif database description file not found ($mat_db)");
    return;
  }
  open MAT_DB, "<$mat_db" or &RSAT::message::Warning( "Cannot read motif database description file file ($mat_db)");;
  while (my $line = <MAT_DB>) {
    chomp($line);
    next if ($line =~ /^;/); ## Skip comment lines
    next if ($line =~ /^#/); ## Skip header line
    next unless ($line =~ /\S/); ## Skip empty lines
    my ($db_name, $format, $file, $descr, $version, $url, $label) = split (/\t/,$line);
    $matrix_db{$db_name}->{'name'} = $db_name;
    $matrix_db{$db_name}->{'format'} = $format || "";
    $matrix_db{$db_name}->{'file'} = $file;
    $matrix_db{$db_name}->{'descr'} = $descr || $db_name;
    $matrix_db{$db_name}->{'version'} = $version || "";
    $matrix_db{$db_name}->{'url'} = $url || "";
    $matrix_db{$db_name}->{'label'} = $label || "";
    # if ($db_name ne lc(db_name)) {
    #   $matrix_db{lc($db_name)} = $matrix_db{$db_name};
    # }
  }

  return %matrix_db;
}

sub supported_motif_databases_2 {
    our  %matrix_db = ();
    ## Load the file containing the path to the databases
    my $mat_db = $ENV{RSAT}."/public_html/motif_databases/db_matrix_files.tab" ;
    unless (-e $mat_db) {
        &RSAT::message::Warning( "Motif database description file not found ($mat_db)");
        return;
    }
    open MAT_DB, "<$mat_db" or &RSAT::message::Warning( "Cannot read motif database description file ($mat_db)");;
    while (my $line = <MAT_DB>) {
        chomp($line);
        next if ($line =~ /^;/); ## Skip comment lines
        next if ($line =~ /^";/); ## Skip comment lines
        next if ($line =~ /^#/); ## Skip header line
        next unless ($line =~ /\S/); ## Skip empty lines
        chomp($line);
        $line =~ s/\r//;
        my ($name, $format, $file, $descr, $version, $url, $category, $db_name) = split (/\t/,$line);        
        if(! defined $matrix_db{$db_name}){ $matrix_db{$db_name} = (); }
        my %db_info = ();
        $db_info{'name'} = $name || "";
        $db_info{'format'} = $format || "";
        $db_info{'file'} = $file;
        $db_info{'descr'} = $descr || $name;
        $db_info{'version'} = $version || "";
        $db_info{'url'} = $url || "";
        $db_info{'category'} = $category || "";
        
        $matrix_db{$db_name}{$name} = \%db_info;        
    }
    
    return %matrix_db;
}


return(1);