#!/usr/local/bin/perl

###############################################################################
# Program     : ShowTICPlot
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This CGI program displays the requested TIC spectrum
#               for a provided fraction
#
# 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 $DATABASE
            );

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

use SBEAMS::Proteomics;
use SBEAMS::Proteomics::Settings;
use SBEAMS::Proteomics::Tables;

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


#use CGI;
#$q = new CGI;


###############################################################################
# Define global variables if any and execute main()
###############################################################################
main();


###############################################################################
# Main Program:
#
# If $sbeams->Authenticate() succeeds, print header, process the CGI request,
# print the footer, and end.
###############################################################################
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,
  ));

  #### Print the header, figure and do what the user want, and print footer
  $sbeamsMOD->printPageHeader();
  processRequests();
  $sbeamsMOD->printPageFooter();

} # end main


###############################################################################
# Process Requests
#
# Test for specific form variables and process the request
# based on what the user wants to do.
###############################################################################
sub processRequests {
    $current_username = $sbeams->getCurrent_username;
    $current_contact_id = $sbeams->getCurrent_contact_id;


    # Enable for debugging
    if (0==1) {
      print "Content-type: text/html\n\n";
      my ($ee,$ff);
      foreach $ee (keys %ENV) {
        print "$ee =$ENV{$ee}=<BR>\n";
      }
      foreach $ee ( $q->param ) {
        $ff = $q->param($ee);
        print "$ee =$ff=<BR>\n";
      }
    }


    #### Only one view available for this program
    printEntryForm();


} # end processRequests



###############################################################################
# Print Entry Form
###############################################################################
sub printEntryForm {

  #### Define some general variables
  my ($i,$element,$key,$value,$sql);

  $sbeams->printUserContext();


  #### Define the parameters that can be passed by CGI
  my @possible_parameters = qw ( fraction_id proteomics_experiment_id );
  my %parameters;


  #### Read in all the passed parameters into %parameters hash
  foreach $element (@possible_parameters) {
    $parameters{$element}=$q->param($element);
  }
  my $apply_action  = $q->param('apply_action');


  #### Resolve the keys from the command line if any
  my ($key,$value);
  foreach $element (@ARGV) {
    if ( ($key,$value) = split("=",$element) ) {
      $parameters{$key} = $value;
    } else {
      print "ERROR: Unable to parse '$element'\n";
      return;
    }
  }


  #### verify that needed parameters were passed
  unless ($parameters{fraction_id}) {
    print "ERROR: not all needed parameters were passed.  This should never ".
      "happen!  Please report this error.<BR>\n";
    return;
  }


  #### Find the corresponding information for this fraction_id
  $sql = qq~
	SELECT fraction_tag,data_location,SB.search_batch_id,
               search_batch_subdir
	  FROM $TBPR_FRACTION F
	 INNER JOIN $TBPR_SEARCH_BATCH SB
               ON ( F.experiment_id = SB.experiment_id )
	 WHERE fraction_id IN ($parameters{fraction_id})
  ~;

  my @fractions = $sbeams->selectSeveralColumns($sql);
  unless (@fractions) {
    print "ERROR: Unable to find any fractions for fraction_id".
      " = '$parameters{fraction_id}'.  This really should never ".
      "happen!  Please report the problem.<BR>\n";
    return;
  }


  #### Provide links to the plots
  foreach my $fraction_ref ( @fractions ) {
    $key = $fraction_ref->[0];
    $value = $fraction_ref->[1];
    my $search_batch_id = $fraction_ref->[2];
    my $search_batch_subdir = $fraction_ref->[3];
    #printf("%22s = %s<BR>\n",$key,$value);
    print "<H3>Fraction: $key</H3>\n";

    my $filename = "$value/../$key.png";
    unless ($filename =~ /^\//) {
      $filename = $RAW_DATA_DIR{Proteomics}."/$filename";
    }

    #print("filename = $filename<BR>\n");
    if ( -e $filename ) {
      print "<IMG SRC=\"$CGI_BASE_DIR/Proteomics/GetImage?".
        "fraction_id=$parameters{fraction_id}&image_type=TIC&search_batch_id=$search_batch_id\"><BR>\n";
    } else {
      print "[PLOTS NOT AVAILABLE FOR THIS FRACTION]<BR>\n";
    }
  }



} # end printEntryForm