#!/usr/local/bin/perl

###############################################################################
# Program     : GetAnnotations
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This CGI program that allows users to
#               browse through annotated proteins very simply
#
# 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 vars qw (%ontology_ids %term_type_ids %relationship_type_ids);

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

use SBEAMS::Ontology;
use SBEAMS::Ontology::Settings;
use SBEAMS::Ontology::Tables;

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


#use CGI;
use CGI::Carp qw(fatalsToBrowser croak);
#$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=>['ProteinStructure_user',
    #  'ProteinStructure_admin','ProteinStructure_readonly','Admin'],
    #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 "xxxx") {
  } else {
    $sbeamsMOD->display_page_header(
      navigation_bar=>$parameters{navigation_bar});
    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="GetAnnotations";
  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{ontology_id} eq $key);
      $optionlist .= "<OPTION VALUE=\"$key\" $flag>$options{$key}</OPTION>\n";
    };

    print qq~
<H2>Browse Ontology</H2>

<P><FORM ACTION="$base_url" METHOD="POST">
Search
<SELECT NAME="ontology_id">
$optionlist
</SELECT> for
<INPUT NAME="search_key" TYPE="text" SIZE="35" VALUE="$parameters{search_key}">
<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


  #### First get a hash of the TermTypes
  $sql = qq~
        SELECT CT.term_name,CT.ontology_term_id
          FROM $TBON_ONTOLOGY_TERM PT
         INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R
               ON ( PT.ontology_term_id = R.subject_term_id )
         INNER JOIN $TBON_ONTOLOGY_TERM CT
               ON ( R.object_term_id = CT.ontology_term_id)
         WHERE PT.ontology_id = 1
           AND PT.term_name = 'TermType'
           AND CT.record_status != 'D'
  ~;
  %term_type_ids = $sbeams->selectTwoColumnHash($sql);


  $sql = qq~
    SELECT ontology_tag,ontology_description,
           OT.ontology_term_id,OT.term_name,OT.term_definition
      FROM $TBON_ONTOLOGY O
      LEFT JOIN $TBON_ONTOLOGY_TERM OT
           ON ( O.ontology_id = OT.ontology_id )
     WHERE OT.term_type_term_id = '$term_type_ids{Root}'
     ORDER BY O.sort_order,OT.sort_order,OT.term_name
  ~;

  my @ontologies = $sbeams->selectSeveralColumns($sql);

  print "<BR><BR><TABLE>\n";


  foreach my $ontology ( @ontologies ) {

    print qq~
      <TR><TD><TABLE>
      <TR><TD ALIGN="LEFT" NOWRAP BGCOLOR="#E0E0E0">$ontology->[0]</TD>
      <TD ALIGN="LEFT" BGCOLOR="#EEEEEE">$ontology->[1]</TD>
      </TR></TABLE></TD></TR>
    ~;

    if (defined($ontology->[2])) {

      expandTree(ontology_term_id => $ontology->[2],
		 current_depth => 1,
		);

    }

    print "<TR><TD>&nbsp;</TD></TR>\n";

  }

  print "</TABLE>\n";


} # end handle_request



###############################################################################
# evalSQL: Callback for translating global table variables to names
###############################################################################
sub evalSQL {
  my $sql = shift;

  return eval "\"$sql\"";

} # end evalSQL



###############################################################################
# expandTree
###############################################################################
sub expandTree {
  my %args = @_;


  #### Process the arguments list
  my $ontology_term_id = $args{'ontology_term_id'}
    || die "ontology_term_id not passed";
  my $current_depth = $args{'current_depth'}
    || die "current_depth not passed";


  my $sql = qq~
    SELECT OT.ontology_term_id,OT.term_name,OT.term_definition,TT.term_name
      FROM $TBON_ONTOLOGY_TERM OT
      LEFT JOIN $TBON_ONTOLOGY_TERM TT
           ON ( OT.term_type_term_id = TT.ontology_term_id )
     WHERE OT.ontology_term_id = '$ontology_term_id'
  ~;

  my @rows = $sbeams->selectSeveralColumns($sql);

  if (scalar(@rows) == 0) {
    print "ERROR: ontology_term_id $ontology_term_id not found!<BR>\n";

  } elsif (scalar(@rows) > 1) {
    print "ERROR: $sql returned too many rows!<BR>\n";

  } else {

    my $term = $rows[0];
    my $indent = 30 * $current_depth;

    print qq~
        <TR><TD><TABLE><TR><TD><IMG SRC="$HTML_BASE_DIR/images/clear.gif" WIDTH="$indent" HEIGHT="1"></TD>
        <TD ALIGN="LEFT" NOWRAP BGCOLOR="#E0E0E0">$term->[3]</TD>
        <TD ALIGN="LEFT" NOWRAP BGCOLOR="#E0E0E0"><A TARGET="TermWin" HREF="ManageTable.cgi?TABLE_NAME=ON_ontology_term&ontology_term_id=$term->[0]">$term->[1]</A></TD>
        <TD ALIGN="LEFT" BGCOLOR="#EEEEEE">$term->[2]</TD>
        </TR></TABLE></TD></TR>
    ~;

    $sql = qq~
      SELECT OT.ontology_term_id,OT.term_name,OT.term_definition,OTT.term_name,
             RT.term_name
        FROM $TBON_ONTOLOGY_TERM ST
        LEFT JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP TR
             ON ( ST.ontology_term_id = TR.subject_term_id )
        LEFT JOIN $TBON_ONTOLOGY_TERM OT
             ON ( TR.object_term_id = OT.ontology_term_id )
        LEFT JOIN $TBON_ONTOLOGY_TERM RT
             ON ( TR.relationship_type_term_id = RT.ontology_term_id )
        LEFT JOIN $TBON_ONTOLOGY_TERM OTT
             ON ( OT.term_type_term_id = OTT.ontology_term_id )
       WHERE ST.ontology_term_id = '$ontology_term_id'
       ORDER BY OT.sort_order,OT.term_name
    ~;

    my @rows = $sbeams->selectSeveralColumns($sql);

    $current_depth++;
    $indent = 30 * $current_depth;

    foreach my $row ( @rows ) {

#      print qq~
#        <TR><TD><TABLE><TR><TD><IMG SRC="$HTML_BASE_DIR/images/clear.gif" WIDTH="$indent" HEIGHT="1"></TD>
#        <TD ALIGN="LEFT" NOWRAP BGCOLOR="#E0E0E0">$row->[3]</TD>
#        <TD ALIGN="LEFT" NOWRAP BGCOLOR="#E0E0E0">$row->[1]</TD>
#        <TD ALIGN="LEFT" BGCOLOR="#EEEEEE">$row->[2]</TD>
#        </TR></TABLE></TD></TR>
#      ~;

      if (defined($row->[0])) {
	expandTree(ontology_term_id => $row->[0],
		   current_depth => $current_depth,
		  );
      }

    }

  }


} # end expandTree