#!/usr/local/bin/perl

###############################################################################
# Program     : ManageTable.cgi
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id: ManageTable.cgi 4503 2006-03-07 23:45:26Z edeutsch $
#
# Description : This CGI program that allows users to
#               manage the contents of a table.
#               This means viewing, inserting, updating,
#               and deleting records.
#
# 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 $utilities $q $dbh $current_contact_id $current_username
             $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE
             $current_work_group_id $current_work_group_name
             $current_project_id $current_project_name
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             $PK_COLUMN_NAME @MENU_OPTIONS);
use DBI;
#use CGI;
use CGI::Carp qw(fatalsToBrowser croak);
use Data::Dumper; 
use SBEAMS::Connection qw($q);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::TableInfo;
#$q = new CGI;
$sbeams = new SBEAMS::Connection;

use SBEAMS::SolexaTrans;
use SBEAMS::SolexaTrans::Settings;
use SBEAMS::SolexaTrans::Tables;
use SBEAMS::SolexaTrans::TableInfo;
use SBEAMS::SolexaTrans::SolexaUtilities;
$sbeamsMOD = new SBEAMS::SolexaTrans;
$utilities = new SBEAMS::SolexaTrans::SolexaUtilities;

$sbeamsMOD->setSBEAMS($sbeams);
$utilities->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);

require 'ManageTable.pllib';



###############################################################################
# Set program name and usage banner for command like use
###############################################################################
$PROG_NAME = $FindBin::Script;
$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 [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()
###############################################################################
# Set maximum post (file upload) to 30 MB
$CGI::POST_MAX = 1024 * 30000;
main();
exit(0);



###############################################################################
# Main Program:
#
# Call $sbeams->InterfaceEntry with pointer to the subroutine to execute if
# the authentication succeeds.
###############################################################################
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,
    #permitted_work_groups_ref=>['Proteomics_user','Proteomics_admin'],
  ));

  #### 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);

  my $project_id = $current_project_id || $sbeams->getCurrent_project_id();


  $TABLE_NAME = $parameters{'TABLE_NAME'}
    || croak "TABLE_NAME not specified."; 

  croak "This TABLE_NAME=$TABLE_NAME cannot be managed by this program."
    unless ($sbeamsMOD->returnTableInfo($TABLE_NAME,
      "ManageTableAllowed"))[0] eq "YES";

  ($CATEGORY) = $sbeamsMOD->returnTableInfo($TABLE_NAME,"CATEGORY");
  ($PROGRAM_FILE_NAME) = $sbeamsMOD->returnTableInfo($TABLE_NAME,
    "PROGRAM_FILE_NAME");
  ($DB_TABLE_NAME) = $sbeamsMOD->returnTableInfo($TABLE_NAME,"DB_TABLE_NAME");
  ($PK_COLUMN_NAME) = $sbeamsMOD->returnTableInfo($TABLE_NAME,
    "PK_COLUMN_NAME");
  @MENU_OPTIONS = $sbeamsMOD->returnTableInfo($TABLE_NAME,"MENU_OPTIONS");

  # Limit the table below based on info
  if ($parameters{where_clause}) {
    if ($parameters{'where_clause'} !~ /project_id/) {
      my $val = $parameters{'where_clause'};
      $val .= "AND project_id = '$project_id'";
      $q->param(-name=>'where_clause', -value=>$val);
    }
  } else {
    if ($parameters{"$PK_COLUMN_NAME"}) {
      $q->param(-name=>'where_clause', -value=>"project_id = '$project_id' AND $PK_COLUMN_NAME = '".$parameters{"$PK_COLUMN_NAME"}."'");
    } else {
      $q->param(-name=>'where_clause', -value=>"project_id = '$project_id'");
    }
  }

  if ($parameters{'slimseq_sample_id'}) {
#    $q->param(-name=>'where_clause', -value=>"slimseq_sample_id = '".$parameters{slimseq_sample_id}."'");
    my $solexa_sample_id = $utilities->check_sbeams_sample(slimseq_id => $parameters{slimseq_sample_id});
    $parameters{solexa_sample_id} = $solexa_sample_id;
    $q->param(-name=>'solexa_sample_id', -value=>"$solexa_sample_id");
  }


  #### Decide what action to take based on information so far
  if ($parameters{"GetFile"} && $parameters{"$PK_COLUMN_NAME"}) {
    getFile(); return;
  }
  $sbeamsMOD->printPageHeader();

  if      ($parameters{action} eq 'VIEWRESULTSET') { printOptions();
  } elsif ($parameters{action} eq 'REFRESH') { printEntryForm();
  } elsif ($parameters{action} eq 'SAVE TEMPLATE') { saveTemplate();
  } elsif ($parameters{action} eq 'SET FIELDS TO THIS TEMPLATE') {
    printEntryForm();
  } elsif ($parameters{action} eq 'DELETE THIS TEMPLATE') {
    deleteTemplate(
      selected_template => $parameters{selected_template},
      program_file_name => $PROGRAM_FILE_NAME,
    );
  } elsif ($parameters{action}) { processEntryForm();
  } elsif ($q->param('apply_action_hidden')) { printEntryForm();
  } elsif ($q->param('ShowEntryForm')) { printEntryForm();
  } elsif ($parameters{"$PK_COLUMN_NAME"}) { printEntryForm();
  } else { printOptions(parameters_ref=>\%parameters); }

  $sbeamsMOD->printPageFooter();


} # end main



###############################################################################
# preFormHook
#
# This is a hook to do some processing before all the lines of data entry
# form have been displayed based on the current table name.  This might be
# used to set some defaults or something.
###############################################################################
sub preFormHook {
  my %args = @_;

  my $query_parameters_ref = $args{'parameters_ref'};


  #### If table XXXX
  if ($TABLE_NAME eq "XXXX") {
    $query_parameters_ref->{YYYY} = 'XXXX'
      unless ($query_parameters_ref->{YYYY});
  }


  #### Otherwise, no special processing, so just return undef
  return;

} # end preFormHook



###############################################################################
# postFormHook
#
# This is a hook to do some processing after all the lines of data entry
# form have been displayed but before the table has been closed based on
# the current table name.
###############################################################################
sub postFormHook {
  my %args = @_;

  my $query_parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$query_parameters_ref};


  #### If table XXXX
  if ($TABLE_NAME eq "XXXX") {
    return "An error of some sort $parameters{something} invalid";
  }


  #### Otherwise, no special processing, so just return undef
  return;

} # end postFormHook



###############################################################################
# preUpdateDataCheck
#
# For certain tables, there are additional checks that should be made before
# an INSERT or UPDATE is performed.
###############################################################################
sub preUpdateDataCheck {
  my %args = @_;

  my $query_parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$query_parameters_ref};


  if ( $parameters{project_id} ) { # General mechanism for tables w/ project_id

    my $errstr = checkProjectPermission( param_ref => $query_parameters_ref,
                                         tname => $TABLE_NAME,
                                         dbtname => $DB_TABLE_NAME );
    return ( $errstr ) if $errstr;
    
  } elsif ($TABLE_NAME eq "XXXX") {

    return "An error of some sort $parameters{something} invalid";

#  } elsif ($TABLE_NAME eq 'ST_SOLEXA_SAMPLE') {
#    return "Solexa Sample ID not specified" if !$parameters{solexa_sample_id};
#    my $errstr = checkPermission(fkey => 'solexa_sample_id',
#                                 fval => $parameters{solexa_sample_id},
#                                 pval => $parameters{solexa_sample_id},
#                                 action => $parameters{action},
#                                 tname => $TABLE_NAME
#                                );

#    return($errstr) if $errstr;

  }

  #### Otherwise, no special processing, so just return empty string
  return '';

} # end preUpdateDataCheck


###############################################################################
# postUpdateOrInsertHook
#
# This is a hook to do some processing after the record has been updated
# or inserted.
###############################################################################
sub postUpdateOrInsertHook {
  my %args = @_;

  my $query_parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$query_parameters_ref};
  my $pk_value = $args{'pk_value'};


  #### If table XXXX
  if ($TABLE_NAME eq "XXXX") {
    return "An error of some sort $parameters{something} invalid";
  }


  #### Otherwise, no special processing, so just return undef
  return;

} # end postUpdateOrInsertHook