#!/usr/local/bin/perl

###############################################################################
# Program     : BrowseRepository
# $Id$
#
# Description : Allows the user to get information about experiments
#               in the PeptideAtlas repository.
#
# 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
             $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::ConsensusSpectrum;

use SBEAMS::Proteomics::Tables;

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

#$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', 'PeptideAtlas_exec'],
        #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
        );


    #### 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();
    }

} # 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();

  #### 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'};


  #### If the apply action was to recall a previous resultset, do it
  my %rs_params = $sbeams->parseResultSetParams('q' => $q);
  my $n_params_found = 0;
  if ($apply_action eq "VIEWRESULTSET") {
    $sbeams->readResultSet(
      resultset_file=>$rs_params{set_name},
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      resultset_params_ref=>\%rs_params,
    );
    $n_params_found = 99;
  }



  #### Set some specific settings for this program
  my $CATEGORY="BrowseRepository";
  my $PROGRAM_FILE_NAME = $PROG_NAME;
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";
  my $help_url = "$CGI_BASE_DIR/help_popup.cgi";

  my ($atlas_build_name, $atlas_build_id);

  if (defined($atlas_build_id) && $atlas_build_id < 0) 
    {
      $parameters{'atlas_build_id'} = $atlas_build_id;
      return;
    }


  my @accessible_project_ids = $sbeams->getAccessibleProjects();
  my $project_string = join( ",", @accessible_project_ids ) || '0';


  #### Get available organisms
  my $sql = qq~
        SELECT organism_id,organism_name
          FROM $TB_ORGANISM
         WHERE 1 = 1
           AND record_status!='D'
 	 ORDER BY organism_name
  ~;
  my $organismOptionlist = $sbeams->buildOptionList(
    $sql,$parameters{'organism_id'});


  if ($sbeams->output_mode() eq 'html') {
    print qq~
        <FORM METHOD="post" NAME="MainForm">
        Select filter criteria for repository experiment list:<BR>
        Organism: <SELECT NAME="organism_id">
          $organismOptionlist</SELECT>
        <P>
       <INPUT TYPE=submit NAME=action VALUE=GO>
       </FORM>
   ~;
  }




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

  #### Build ATLAS_BUILD constraint
  my $organism_id_clause = $sbeams->parseConstraint2SQL(
        constraint_column=>"s.organism_id",
        constraint_type=>"int_list",
        constraint_name=>"Organism",
        constraint_value=>$parameters{organism_id} );
  return if ($organism_id_clause eq '-1');


  #### Define the desired columns in the query
  #### [friendly name used in url_cols,SQL,displayed column title]
  my @column_array = (
    ["sample_accession","S.sample_accession","Sample Accession"],
    ["organism_name","O.organism_name","Organism Name"],
    ["sample_tag","S.sample_tag","Sample Tag"],
    ["sample_title","S.sample_title","Sample Title"],
  );


  #### Build the columns part of the SQL statement
  my %colnameidx = ();
  my @column_titles = ();
  my $columns_clause = $sbeams->build_SQL_columns_list(
    column_array_ref=>\@column_array,
    colnameidx_ref=>\%colnameidx,
    column_titles_ref=>\@column_titles
  );


  #### Define the SQL statement
  $sql = qq~
         SELECT $columns_clause
         FROM $TBAT_SAMPLE S
         LEFT JOIN $TB_ORGANISM O
          ON ( S.organism_id = O.organism_id )
         WHERE 1 = 1
           AND S.is_public = 'Y'
            $organism_id_clause
        ORDER BY organism_name,sample_tag
  ~;

  #### Define the hypertext links for columns that need them
  %url_cols = (
  );

  #### Define the hidden columns
  %hidden_cols = (
  );

  #########################################################################
  #### If QUERY or VIEWRESULTSET was selected, display the data
  if ($apply_action =~ /(QUERY|GO|VIEWRESULTSET)/) {

    #### Show the SQL that will be or was executed
    $sbeams->display_sql(sql=>$sql) if ($show_sql);

    #### If the action contained QUERY, then fetch the results from
    #### the database
    if ($apply_action =~ /(QUERY|GO)/i) {

      #### Fetch the results from the database server
      $sbeams->fetchResultSet(
        sql_query=>$sql,
        resultset_ref=>$resultset_ref,
      );

      #### Store the resultset and parameters to disk resultset cache
      $rs_params{set_name} = "SETME";
      $sbeams->writeResultSet(
        resultset_file_ref=>\$rs_params{set_name},
        resultset_ref=>$resultset_ref,
        query_parameters_ref=>\%parameters,
        resultset_params_ref=>\%rs_params,
        query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME",
      );
    }


    #### Display the resultset
    $sbeams->displayResultSet(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      rs_params_ref=>\%rs_params,
      url_cols_ref=>\%url_cols,
      hidden_cols_ref=>\%hidden_cols,
      max_widths=>\%max_widths,
      column_titles_ref=>\@column_titles,
      base_url=>$base_url,
    );

    #### Display the resultset controls
    $sbeams->displayResultSetControls(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      rs_params_ref=>\%rs_params,
      base_url=>$base_url,
    );


  #### If QUERY was not selected, then tell the user to enter some parameters
  } else {
    if ($sbeams->invocation_mode() eq 'http') {
      print "Click [GO] to execute the search<BR>\n";
    } else {
      print "Set action=GO to execute the search\n";
    }
  }


} # end handle_request