#!/usr/local/bin/perl

###############################################################################
# Program     : Help
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This script authenticates the user, and then
#               displays the specified help information.
#
# SBEAMS is Copyright (C) 2000-2005 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation.  It is provided
# WITHOUT ANY WARRANTY.  See the full description of GPL terms in the
# LICENSE file distributed with this software.
#
###############################################################################


###############################################################################
# Set up all needed modules and objects
###############################################################################
use strict;
use Getopt::Long;
use FindBin;

use lib "$FindBin::Bin/../../lib/perl";
use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username
             $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $TESTONLY
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             @MENU_OPTIONS);

use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Cytometry;
use SBEAMS::Cytometry::Settings;
use SBEAMS::Cytometry::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::Cytometry;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);


#use CGI;
#$q = new CGI;


###############################################################################
# Set program name and usage banner for command line use
###############################################################################
$PROG_NAME = $FindBin::Script;
$USAGE = <<EOU;
Usage: $PROG_NAME [OPTIONS] key=value key=value ...
Options:
  --verbose n         Set verbosity level.  default is 0
  --quiet             Set flag to print nothing at all except errors
  --debug n           Set debug flag to level n
  --testonly          Set testonly flag which simulates INSERTs/UPDATEs only

 e.g.:  $PROG_NAME --verbose 2 keyword=value

EOU

#### Process options
unless (GetOptions(\%OPTIONS,"verbose:s","quiet","debug:s","quiet")) {
  print "$USAGE";
  exit;
}

$VERBOSE = $OPTIONS{"verbose"} || 0;
$QUIET = $OPTIONS{"quiet"} || 0;
$DEBUG = $OPTIONS{"debug"} || 0;
$TESTONLY = $OPTIONS{"testonly"} || 0;
if ($DEBUG) {
  print "Options settings:\n";
  print "   VERBOSE = $VERBOSE\n";
  print "     QUIET = $QUIET\n";
  print "     DEBUG = $DEBUG\n";
  print "  TESTONLY = $TESTONLY\n";
}


###############################################################################
# Set Global Variables and execute main()
###############################################################################
$PROGRAM_FILE_NAME = 'Help';
main();
exit(0);


###############################################################################
# Main Program:
#
# Call $sbeams->Authenticate() and exit if it fails or continue if it works.
###############################################################################
sub main {

  #### Do the SBEAMS authentication and exit if a username is not returned
  exit unless ($current_username = $sbeams->Authenticate(
    #permitted_work_groups_ref=>['Proteomics_user','Proteomics_admin',
    #  'Proteomics_readonly'],
    #connect_read_only=>1,
    #allow_anonymous_access=>1,
  ));


  #### Read in the default input parameters
  my %parameters;
  my $n_params_found = $sbeams->parse_input_parameters(
    q=>$q,parameters_ref=>\%parameters);
  #$sbeams->printDebuggingInfo($q);


  #### Process generic "state" parameters before we start
  $sbeams->processStandardParameters(parameters_ref=>\%parameters);


  #### Decide what action to take based on information so far
  if ($parameters{action} eq "???") {
    # Some action
  } else {
    $sbeamsMOD->display_page_header();
    handle_request(ref_parameters=>\%parameters);
    $sbeamsMOD->display_page_footer();
  }


} # end main



###############################################################################
# Handle Request
###############################################################################
sub handle_request {
  my %args = @_;


  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  my %parameters = %{$ref_parameters};


  #### Show current user context information
  $sbeams->printUserContext();
  $current_contact_id = $sbeams->getCurrent_contact_id();

  my $document;


  #### If no document was specified, complain (ideally list all)
  unless ($parameters{document}) {
    print "ERROR: Document unspecified<BR>\n";
    return;
  }


  #### Help: Proteomics Tutorial
my $document = "SampleNameConvention";

    if ($parameters{document} eq $document){
      
      
     #print out the list of links
#    $sbeamsMOD->documentation_list();
#   }elsif ($document = grep { $parameters{document} eq ($_) } @documents){
 #      $document = $parameters{document};

#    my $document_file = "$PHYSICAL_BASE_DIR/doc/Proteomics/$document.php";
    my $document_file = "$PHYSICAL_BASE_DIR/doc/Cytometry/$document.php";
    if (-e $document_file) {
      open(INFILE,$document_file)
	|| die("ERROR: Unable to read $document_file");

      my $is_content = 0;
      my $page = '';
      while (my $line = <INFILE>) {

	if ($is_content) {
	  if ($line =~ /^<?php/) {
	    last;
	  }

	  print $line;
    $page .= $line;

	} else {

	  if ($line =~ /Main Page Content/) {
	    $is_content = 1;
	  }

	}

      }

      close(INFILE);
      $log->debug( $page);


    } else {
      print "ERROR: Unable to find document $document_file\n";
    }
  } else {
    print "ERROR: Unrecognized document $parameters{document}\n";
  }


  return;


} # end handleResquest