#!/usr/local/bin/perl

###############################################################################
# Program     : GetPeptide
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id: GetPeptide,v 1.1 2004/08/10 07:32:00 edeutsch Exp $
#
# Description : This program that allows users to
#               view all the information for a given peptide in the context
#               of a certain build.
#
# SBEAMS is Copyright (C) 2000-2003 by Eric Deutsch
# 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
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             @MENU_OPTIONS);
##use CGI::Carp qw(fatalsToBrowser croak);

use SBEAMS::Connection;
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;

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


use CGI;
$q = new CGI;


###############################################################################
# Set program name and usage banner for command like 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

 e.g.:  $PROG_NAME [OPTIONS] [keyword=value],...

EOU

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

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


###############################################################################
# Set Global Variables and execute main()
###############################################################################
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=>['PeptideAtlas_user','PeptideAtlas_admin',
      'PeptideAtlas_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};


  #### Define some generic varibles
  my ($i,$element,$key,$value,$line,$result,$sql);


  #### Define some variables for a query and resultset
  my %resultset = ();
  my $resultset_ref = \%resultset;
  my (%url_cols,%hidden_cols,%max_widths,$show_sql);


  #### Read in the standard form values
  my $apply_action  = $parameters{'action'} || $parameters{'apply_action'};
  my $TABLE_NAME = $parameters{'QUERY_NAME'};


  #### Set some specific settings for this program
  my $PROGRAM_FILE_NAME="GetPeptide";
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";


  #### Get the columns and input types for this table/query
  my @columns = ( 'search_scope','search_key' );
  my %input_types = ( 'optionlist','text' );


  #### Read the input parameters for each column
  my $n_params_found = $sbeams->parse_input_parameters(
    q=>$q,parameters_ref=>\%parameters,
    columns_ref=>\@columns,input_types_ref=>\%input_types);


  #### If the apply action was to recall a previous resultset, do it
  my %rs_params = $sbeams->parseResultSetParams(q=>$q);
  if ($apply_action eq "VIEWRESULTSET") {
    $sbeams->readResultSet(resultset_file=>$rs_params{set_name},
        resultset_ref=>$resultset_ref,query_parameters_ref=>\%parameters);
    $n_params_found = 99;
  }


  #### Set some reasonable defaults if no parameters supplied
  unless ($n_params_found) {
  }


  #### Apply any parameter adjustment logic
  #$parameters{display_options} = 'ShowSQL';


  #### Display the user-interaction input form
  if ($sbeams->output_mode() eq 'html') {
    my @options = ( 'GeneSymbol','ORFName','FullGeneName','ECNumbers','All' );
    my %options = ( 'GeneSymbol' => 'Gene Symbol',
		    'ORFName' => 'ORF Name',
		    'FullGeneName' => 'Full Gene Name',
		    'ECNumbers' => 'EC Number',
		    'All' => 'All Attributes',
		  );

    #### Build the option list
    my $optionlist = '';
    foreach my $key ( @options ) {
      my $flag = '';
      $flag = 'SELECTED' if ($parameters{search_scope} eq $key);
      $optionlist .= "<OPTION VALUE=\"$key\" $flag>$options{$key}</OPTION>\n";
    };

    print qq~
<tr><td><span class="sub_header">BROWSE THE PROTEOME</span></td></tr>

<tr><td height="1"><img src="$HTML_BASE_DIR/images/bg_Nav.gif" width="518" height="1" border="0"></td></tr>
<tr><td height="5"><img src="$HTML_BASE_DIR/images/clear.gif" width="1" height="1" border="0"></td></tr>

<tr><td>
<P><FORM ACTION="$base_url" METHOD="POST">
Search
<SELECT NAME="search_scope">
$optionlist
</SELECT> for
<INPUT NAME="search_key" TYPE="text" SIZE="35" VALUE="$parameters{search_key}">
<INPUT NAME="biosequence_set_id" TYPE="hidden" VALUE="$parameters{biosequence_set_id}">
<INPUT TYPE="submit" NAME="action" VALUE="GO">
</FORM></P>
    ~;
  }


  #### Finish the upper part of the page and go begin the full-width
  #### data portion of the page
#  $sbeams->display_page_footer(close_tables=>'YES',
#    separator_bar=>'YES',display_footer=>'NO')
#    unless ( $parameters{display_options} =~ /SequenceFormat/ &&
#      $apply_action =~ /HIDE/ );



  #########################################################################
  #### Process all the constraints

  #### Build BIOSEQUENCE_SET constraint
  my $form_test = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_set_id",
    constraint_type=>"int_list",
    constraint_name=>"BioSequence Set",
    constraint_value=>$parameters{biosequence_set_id} );
  return if ($form_test eq '-1');

  #### Verify that the selected biosequence_sets are permitted
  if ($parameters{biosequence_set_id}) {
    my $sql = qq~
      SELECT biosequence_set_id,project_id
	FROM $TBAT_BIOSEQUENCE_SET
       WHERE biosequence_set_id IN ( $parameters{biosequence_set_id} )
	 AND record_status != 'D'
    ~;
    my %project_ids = $sbeams->selectTwoColumnHash($sql);
    my @accessible_project_ids = $sbeams->getAccessibleProjects();
    my %accessible_project_ids;
    foreach my $id ( @accessible_project_ids ) {
      $accessible_project_ids{$id} = 1;
    }

    my @input_ids = split(',',$parameters{biosequence_set_id});
    my @verified_ids;
    foreach my $id ( @input_ids ) {

      #### If the requested biosequence_set_id doesn't exist
      if (! defined($project_ids{$id})) {
	$sbeams->reportException(
          state => 'ERROR',
          type => 'BAD CONSTRAINT',
          message => "Non-existent biosequence_set_id = $id specified",
        );

      #### If the project for this biosequence_set is not accessible
      } elsif (! defined($accessible_project_ids{$project_ids{$id}})) {
	$sbeams->reportException(
          state => 'ERROR',
          type => 'PERMISSION DENIED',
          message => "Your current privilege settings do not allow you to access biosequence_set_id = $id.  See project owner to gain permission.",
        );

      #### Else, let it through
      } else {
	push(@verified_ids,$id);
      }

    }

    #### Set the input constraint to only allow that which is valid
    $parameters{biosequence_set_id} = join(',',@verified_ids);

  }

  #### If no valid biosequence_set_id was selected, stop here
  unless ($parameters{biosequence_set_id}) {
    $sbeams->reportException(
      state => 'ERROR',
      type => 'INSUFFICIENT CONSTRAINTS',
      message => "You must select at least one valid Biosequence Set",
    );
    return;
  }

  #### Build BIOSEQUENCE_SET constraint
  my $biosequence_set_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_set_id",
    constraint_type=>"int_list",
    constraint_name=>"BioSequence Set",
    constraint_value=>$parameters{biosequence_set_id} );
  return if ($biosequence_set_clause eq '-1');


  #### Build SEARCH SCOPE constraint
  my $search_scope_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.search_scope",
    constraint_type=>"plain_text",
    constraint_name=>"Search Scope",
    constraint_value=>$parameters{search_scope},
  );
  return if ($search_scope_clause eq '-1');


  #### Build SEARCH KEY constraint
  my $search_key_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.search_key",
    constraint_type=>"plain_text",
    constraint_name=>"Search Key",
    constraint_value=>$parameters{search_key},
  );
  return if ($search_scope_clause eq '-1');




  #### Put full peptide display here or in a subroutine.




} # end handle_request



###############################################################################
# evalSQL
#
# Callback for translating Perl variables into their values,
# especially the global table variables to table names
###############################################################################
sub evalSQL {
  my $sql = shift;

  return eval "\"$sql\"";

} # end evalSQL

