#!/usr/local/bin/perl

###############################################################################
# Program     : show_est_library
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This CGI program that allows users to
#               a summary of interesting EST Libraries.
#
###############################################################################


###############################################################################
# Set up all needed modules and objects
###############################################################################
use strict;
use Getopt::Long;

use lib qw (../../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);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;

use SBEAMS::BEDB;
use SBEAMS::BEDB::Settings;
use SBEAMS::BEDB::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::BEDB;
$sbeamsMOD->setSBEAMS($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 = "get_annotation";
$USAGE = <<EOU;
Usage: $PROG_NAME [OPTIONS] key=value kay=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 annotation_id=111 rs_output_format=tsv

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(
    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);


  #### 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'}
     || "QUERY";
  my $TABLE_NAME = $parameters{'QUERY_NAME'};


  #### Set some specific settings for this program
  my $CATEGORY="Show EST Libraries";
  $TABLE_NAME="BE_show_est_library" unless ($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);


  #### 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) {
  }


  #### Finish the upper part of the page and go begin the full-width
  #### data portion of the page
  #$sbeams->display_page_footer(close_tables=>'YES',
  #  separator_bar=>'YES',display_footer=>'NO');
  if ($sbeams->output_mode() eq 'interactive' ||
      $sbeams->output_mode() eq 'html') {
    print qq~
      <BR>The Brain Expression database contains data from the following
      EST Libraries:<BR>
      <BR>
    ~;
  }


  #### Define the desired columns
  my @column_array = (
    ["est_library_id","EL.est_library_id","est_library_id"],
    ["library_name","EL.library_name","Library Name"],
    ["description","EL.description","Description"],
    ["unigene_library_id","EL.unigene_library_id","unigene_library_id"],
    ["n_chromats","EL.n_chromats","Available Chromats"],
    ["n_good_ests","EL.n_good_ests","Good ESTs"],
    ["n_distinct_genes","EL.n_distinct_genes","Distinct Genes"],
    ["processed_date","SUBSTRING(CONVERT(varchar(25),EL.processed_date,121),1,10)","Date Processed"],
    ["keywords","EL.keywords","Keywords"],
  );



  #### 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
  );


  $sql = qq~
    SELECT $columns_clause
      FROM $TBBE_EST_LIBRARY EL
     WHERE n_chromats > 0
     ORDER BY library_name
   ~;


  %url_cols = ('Library Name' => "http://www.ncbi.nlm.nih.gov/cgi-bin/UniGene/lib?ORG=Hs&LID=\%$colnameidx{unigene_library_id}V",
               'Library Name_ATAG' => 'TARGET="Win2"',
               'Distinct Genes' => "$CGI_BASE_DIR/$SBEAMS_SUBDIR/get_annotation?est_library_id=\%$colnameidx{est_library_id}V&sort_order=8&apply_action=HIDEQUERY",
               'Distinct Genes_ATAG' => 'TARGET="Win2"',
               'Available Chromats' => "$CGI_BASE_DIR/$SBEAMS_SUBDIR/get_est?est_library_id=\%$colnameidx{est_library_id}V&apply_action=HIDEQUERY",
               'Available Chromats_ATAG' => 'TARGET="Win2"',
  );

  %hidden_cols = ('est_library_id' => 1,
                  'unigene_library_id' => 1,
   );



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

    #### Display the resultset
    $sbeams->displayResultSet(rs_params_ref=>\%rs_params,
        url_cols_ref=>\%url_cols,hidden_cols_ref=>\%hidden_cols,
        max_widths=>\%max_widths,resultset_ref=>$resultset_ref,
        column_titles_ref=>\@column_titles,
        table_width=>'fit_to_page',
        row_color_scheme_ref=>$sbeamsMOD->getTableColorScheme(),
    );


    #### Display the resultset controls
    #$sbeams->displayResultSetControls(rs_params_ref=>\%rs_params,
    #    resultset_ref=>$resultset_ref,query_parameters_ref=>\%parameters,
    #    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 "<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 global table variables to names
###############################################################################
sub evalSQL {
  my $sql = shift;

  return eval "\"$sql\"";

} # end evalSQL