#!/usr/local/bin/perl

###############################################################################
# Program     : GetPABSTList
#
# Description : form to retrieve peptides and MS/MS fragment ions given
#               constraints and send request to viewer
###############################################################################


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

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

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::PeptideAtlas;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR( 'PeptideAtlas' );
my $best_peptide = new SBEAMS::PeptideAtlas::BestPeptideSelector;
$best_peptide->setAtlas( $sbeamsMOD );
$best_peptide->setSBEAMS( $sbeams );


###############################################################################
# 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";
}

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(
        allow_anonymous_access=>1,
    ));


    #### Read in the default input parameters
    my %parameters;

    $parameters{uploaded_file_not_saved} = 1;

    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 
    {
        my $project_id = $sbeamsMOD->getProjectID(
            atlas_build_id => $parameters{atlas_build_id}
        );

        $sbeamsMOD->display_page_header(project_id => $project_id);

        handle_request(ref_parameters=>\%parameters);

        $sbeamsMOD->display_page_footer();
    }

    #### 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');

} # 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
    print "<BR>\n" if ($sbeams->output_mode() eq 'html');

    #$sbeams->printUserContext();

    #### Get the HTML to display the tabs
    my $tabMenu = $sbeamsMOD->getTabMenu(
        parameters_ref => \%parameters,
        program_name => $PROG_NAME,
    );

    print $tabMenu->asHTML() if ($sbeams->output_mode() eq 'html');

    #### Define some generic variables
    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 $CATEGORY="Get PABST List";

    $TABLE_NAME="AT_GetPABSTList" unless ($TABLE_NAME);

    ($PROGRAM_FILE_NAME) =
        $sbeamsMOD->returnTableInfo($TABLE_NAME,"PROGRAM_FILE_NAME");

    my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";

    #### Get the columns and input types for this table/query
    my @columns = $sbeamsMOD->returnTableInfo($TABLE_NAME,"ordered_columns");

    my %input_types = 
        $sbeamsMOD->returnTableInfo($TABLE_NAME,"input_types");


    #### 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);
     #$sbeams->printDebuggingInfo($q);


    #### If the apply action was to recall a previous resultset, do it
    my %rs_params = $sbeams->parseResultSetParams(q=>$q);

    #### Set some reasonable defaults if no parameters supplied
    unless ($n_params_found) 
    {
        $parameters{input_form_format} = "minimum_detail";
    }

    ##Input form:  action is set by PROGRAM_FILE_NAME, so sub it w/ display page:
    $sbeams->collectSTDOUT();
    $sbeams->display_input_form(
        TABLE_NAME=>$TABLE_NAME,
        CATEGORY=>$CATEGORY,
        apply_action=>$apply_action,
        PROGRAM_FILE_NAME=>"$CGI_BASE_DIR/$SBEAMS_SUBDIR/ViewPABSTList",
        parameters_ref=>\%parameters,
        input_types_ref=>\%input_types,
        mask_user_context=> '1',
    );
    my $form = $sbeams->fetchSTDOUT();
    my $id = 'ID="protein_name_constraint"';
    $form =~ s/(NAME=\"protein_name_constraint\")/$1 $id/;



    my $sub_form = $best_peptide->get_change_form( form_only => 1, hide_buttons => 1 );
    $sub_form =~ s/tbl_hidden/tbl_visible/gm;
   
    $form =~ s/(\<INPUT TYPE="hidden" NAME="QUERY_NAME" VALUE="AT_GetPABSTList"\>)/$1<BR>$sub_form/gm;
    $form =~ s/\<\/TABLE\>/<TR><TD COLSPAN=3>$sub_form<\/TD><\/TR><\/TABLE>/i;
#    $form .= "<TR><TD COLSPAN=3>$sub_form</TD></TR>\n";
    $form .= "<TR><TD VALIGN=TOP><B>Adjust penalties:</B></TD><TD BGCOLOR=E0E0E0></TD><TD>$sub_form</TD></TR>\n";

    print qq~
    $form
    ~;
#    <TR><TD COLSPAN=3>$sub_form</TD></TR>

    #### Display the form action buttons
    $sbeams->display_form_buttons(TABLE_NAME=>$TABLE_NAME);

} # end handle_request