#!/usr/local/bin/perl

###############################################################################
# Program     : IntegrateResultsets
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This program that allows users to
#               select several different resultsets of different types and
#               send them to Cytoscape for integration
#
# 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);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;

$sbeams = new SBEAMS::Connection;

#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()
###############################################################################
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=>['xxx','yyy'],
    #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 (defined($parameters{action}) && $parameters{action} eq "???") {
    # Some action
  } else {
    $sbeams->display_page_header();
    handle_request(ref_parameters=>\%parameters);
    $sbeams->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 $CATEGORY="Integrate Resultsets";
  $TABLE_NAME="IntegrateResultsets" unless ($TABLE_NAME);
  ($PROGRAM_FILE_NAME) =
    $sbeams->returnTableInfo($TABLE_NAME,"PROGRAM_FILE_NAME");
  my $base_url = "$CGI_BASE_DIR/$PROGRAM_FILE_NAME";


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


  #### 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,
      resultset_params_ref=>\%rs_params,
    );
    $n_params_found = 99;
  }


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


  #### Apply any parameter adjustment logic
  $parameters{m} = 'merge';


  #### Display the user-interaction input form
  $sbeams->display_input_form(
    TABLE_NAME=>$TABLE_NAME,
    CATEGORY=>$CATEGORY,
    apply_action=>$apply_action,
    #PROGRAM_FILE_NAME=>$PROGRAM_FILE_NAME,
    PROGRAM_FILE_NAME=>"http://db.systemsbiology.net/cytoscape/sbeamsTest",
    #PROGRAM_FILE_NAME=>"http://hazel.systemsbiology.net:8080/cytoscape/sbeamsTest",
    #PROGRAM_FILE_NAME=>"$SERVER_BASE_DIR/cgi-bin/printenv",
    parameters_ref=>\%parameters,
    input_types_ref=>\%input_types,
  );


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


  #### 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');



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



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

    if (defined($parameters{interactions_resultset})) {
      print "IN_rs=$parameters{interactions_resultset}<BR>\n";
    }

    if (defined($parameters{microarray_resultset})) {
      print "MA_rs=$parameters{microarray_resultset}<BR>\n";
    }

    if (defined($parameters{proteomics_resultset})) {
      print "PR_rs=$parameters{proteomics_resultset}<BR>\n";
    }




  #### If QUERY was not selected, then tell the user to enter some parameters
  } else {
    if ($sbeams->invocation_mode() eq 'http') {
      print "<H4>Select parameters above and press QUERY</H4>\n";
    } else {
      print "You need to supply some parameters to contrain the query\n";
    }
  }


} # 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


###############################################################################
# display_form_buttons
#
# Display the parameter form buttons for this particular table or query
###############################################################################
sub display_form_buttons {
  #my $self = shift;
  my %args = @_;


  #### Process the arguments list
  my $TABLE_NAME = $args{'TABLE_NAME'};


  #### If the output mode is not html, then we don't want anything
  if ($sbeams->output_mode() ne 'html') {
    return;
  }


  #### Show the QUERY, REFRESH, and Reset buttons
  print qq~
      <TR><TD COLSPAN=2>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      <INPUT TYPE="submit" NAME="action" VALUE="Cytoscape">
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      <INPUT TYPE="submit" NAME="action" VALUE="Cytoscape test">
      <INPUT TYPE="hidden" NAME="username" VALUE="$current_username">
       </TR></TABLE>
       </FORM>
  ~;

} # end display_form_buttons