<%once>
my $none;
my $groupname = undef;
use Carp::Assert;
use WorkingSet::SetContainer;
use SearchUtil;
</%once>
<%perl>
my $session = $m->session();
#warn Dumper %ARGS2,"ARGS@@@@@" if DEBUG;
my $orig_action = $ARGS2{action};
warn "original action is $orig_action" if DEBUG;

my $dbh = pgconnect();

my @time = (localtime);

$| = 1;

my $refreshNavBar=0;

#make sure the user has a working set object.
my $workingSet = resultUtil::prep_working_set($session->{workingset});

#there are two pulldown menus.
$ARGS2{switch} = $ARGS2{switch1} if $ARGS2{switch1};
$ARGS2{switch} = $ARGS2{switch2} if $ARGS2{switch2};

#user is downloading a file.

my $genome_ws_view;
if($ARGS2{setview})
  {
    warn "setview is set" if DEBUG;
    $workingSet->setview($ARGS2{setview});
    $genome_ws_view = 1 if $ARGS2{setview} eq "S";
  }

if($ARGS2{"download"})
  {
    warn "download" if DEBUG;
    #warn Dumper "ARGS2", %ARGS2;
    %ARGS2 = $m->comp('.download', display => $ARGS2{download});
    
  }
elsif(not %ARGS2)
  {
    #warn "getting last args" if DEBUG;
   #warn Dumper %ENV, "ENV";
    # don't get last args if they just downloaded a file
    if($ENV{SCRIPT_URI} =~ /search|html$/)
      {
        #then don't reset the args.
      }
    else
#    unless($session->{download} eq "excel")
      {
        %ARGS2 = $m->comp('.need_args');
      }
  }
elsif($ARGS2{switch})
{
  # just like Apple. do the switch.
  
  
  #warn "switching $ARGS2{switch}" if DEBUG;


  # check that there is a SetContainer.
  if(ref $session->{set_container} eq "WorkingSet::SetContainer")
    {
      # double check the set exists.
      if($session->{set_container}->contains($ARGS2{switch}))
        {
          $session->{set_container}->active($ARGS2{switch});
          $session->{working_set} = $session->{workingset} = $workingSet = $session->{set_container}->get_active;
          %ARGS2 = %{$session->{last}} if ref $session->{last} eq "HASH" && scalar keys %ARGS2 == 1;
        }
      else { warn "not switching - set doesn't exist anymore" if DEBUG }
    }
  else {warn "not switching - no set container" if DEBUG};
}


#do this after we've updated to a new set if they switched sets.
$genome_ws_view =  $workingSet->setview eq "S" && $orig_action =~ /view/ ? 1 : 0;
#warn Dumper $workingSet, "WOKRINGSET";
#warn Dumper "set view?", $workingSet->setview,$ARGS2{action} if DEBUG;

if($ARGS2{"update_ws"})
  {
    warn "updating working set" if DEBUG;
    %ARGS2 = $m->comp('.working_set', ws => $ARGS2{ws}, workingSet => $workingSet, checkbox => $ARGS2{checkbox}, action => $ARGS2{action});
    #warn Dumper %ARGS2, "args 2";
    $workingSet = $session->{working_set};
    #if we just added something to a set, so cached search results.
 }

my %results;
my $comp;
my $using_cache;
if($ARGS2{action} =~ "prev_")
  {
    warn "using cached search results";
    $using_cache=1;
    ($comp, %results) = SearchUtil::get_saved_search($session, $ARGS2{action});
    #warn "comp is $comp";
  }
else
  {
    for(qw(offset mine omitfrags print translate nosqueeze))
      {
        $ARGS2{$_} ||= 0;
      }
    #some other default values.
    my $relArrRef;
    $ARGS2{"nucorpro"} = "nuc" unless($ARGS2{"nucorpro"});
    
    
    #save the order preference for later in the session for the views and such.
    $ARGS2{orderby} = resultUtil::getOrderBy($ARGS2{orderby}, $session->{orderby});
    #warn "ORDERBY is $ARGS2{orderby}" if $DEBUG;
    
    $ARGS2{"num"} = 100 unless  ($ARGS2{"num"});                
    
    # displayed stuff
    
    my  $layerToShow = 0; # default layer
    #   }
    #print STDERR "groupname:$session->{user}\n";
    if ($ENV{'HTTPS'} && $ENV{'HTTPS'} =~/on/i) {
      $groupname = uc $session->{'user'};
    }
    
    #probably need to make sure they are viewing the working set as well.
    # not sure if it does make sure of it.
    
    $session->{genome_ws_view} = $genome_ws_view;
    warn "genome ws view" if $genome_ws_view;
    $ARGS2{action} = "genome" if $workingSet->setview eq "S" && $ARGS2{action} =~ /view/;
    warn "action is $ARGS2{action}";
    #warn Dumper %ARGS2,"ARGS2";
    # returns a ViewResult, AlignmentResult2 or SearchResult object
my $action_obj = Search::ResultFactory->new($ARGS2{action}, \%ARGS2);
    
    for(qw (orderby omitfrags showother))
      {
        $session->{$_} = $ARGS2{$_};
      }

    my %minisession;
    my @mini_keys = qw(bigtotal showother where top alignment_links);
    @minisession{@mini_keys} = @{$session}{@mini_keys};
    
    for(qw(session dbh r env_https workingset working_set set_container xml))
      {
        delete $ARGS2{$_};
      }
    #warn Dumper $ARGS2{scope}, $ARGS2{superscope};
    $ARGS2{scope} = "checked" if $ARGS2{superscope};
    $ARGS2{scope} = "all" if $ARGS2{superscope} eq "all";


    my @checked = $m->comp("/components/get_set_choice.cmp", scope => $ARGS2{scope}, setlist => $ARGS2{superscope});

    #have to be careful, the %ARGS2 may contain some of these other values. 
    my @uri = split(/\//, $r->uri);
    #warn Dumper $workingSet;

    assert($workingSet->isa("WorkingSet"), "need working set") if DEBUG;


    my %arguments = ("dbh" => $dbh, 
                     "session" => \%minisession,
                     "r" => $r,
                     "groupname" => $groupname,
                     "env_https" => $ENV{HTTPS},
                     workingset => $workingSet,
                     uri => $uri[0]."/search/index.html",
                     user_agent => $ENV{HTTP_USER_AGENT},
                     genome_detail => $genome_ws_view,
                    );
    
    $arguments{checked} = \@checked if @checked;
    
    my $time = time;
    warn "startingprepareResult", ref $action_obj if DEBUG;
    
    # do the actual work
  %results = $action_obj->prepareResult(%arguments);
    $comp = $action_obj->{component};


    # handle the results
    #warn Dumper %results;
    if(exists $results{error})
      {
        warn "error calling error page. $results{error}";
        $m->comp("/components/error.cmp", message => $results{error});
        Apache::exit;
      }
    elsif(exists $results{message})
      {
        $m->comp("/components/nothing.cmp", message => $results{message});
        Apache::exit;
      }
    delete $ARGS2{download};
    delete $ARGS2{display};
    #session and/or ARGS2 may need updating now. 
    if(ref $results{session} eq "HASH"){
      
      for(keys %{$results{session}})
        {
          $session->{$_} = $results{session}->{$_} unless ref $results{session}->{$_};
        }
    }
    
    $session->{last} = \%ARGS2;
    
    @ARGS2{keys %{$results{args}}} = values %{$results{args}} if (ref($results{args}) eq "HASH");
    
    $session->{alignment_links} = $results{results}->{alignment_links} if ref $results{results} eq "HASH" && exists $results{results}->{alignment_links};
    
    
    
    for(keys %ARGS2, "clip", "alnseg", "protein", "pos3", "action", "hspecies", "colorcode", "doprosite", "prosite" ,"repeat", "neg", "show_length")
      {
        $session->{$_} = $ARGS2{$_};
      }
}

#
# The real output at last.
#
    $m->comp($comp, args => $results{results});
#

#
# If we just performed a search, save the results so we can save a db query later if they want to view the results again.
#

if($ARGS2{action} =~ /^(genome|search)/ && $ARGS{download} ne "excel")
  {
$session->{download} = undef;
    SearchUtil::save_search_results($session, $ARGS2{action}, $results{results}, $comp);

    assert(ref $session->{"prev_$ARGS2{action}"}, "didn't cache") if DEBUG;
    #warn "SET the CACHE!" if DEBUG;
  }
</%perl>
<%cleanup>
$dbh->disconnect() if $dbh;
</%cleanup>
<%flags>
inherit=>undef
</%flags>
<%def .download><%perl>
# have to have the def block on the same line as the perl block  or else we get a newline in the file.
  my $session = $m->session;
  #set args from the session
  
  my @sessionArgs = grep(!/display/,keys %{$session});
  %ARGS = ();
  %ARGS= %{$session->{last}} if ref $session->{last} eq "HASH";
  
  $ARGS{display} = $display;
  # want the session args that were just used before the download request.
  return %ARGS;
</%perl>
<%args>
$display
</%args></%def>
<%def .need_args><%perl>
my $session = $m->session;
 # if there are no arguments, reuse the old ones from the session.

   # it would be nice to just get the keys that should be ARGS2, not all that other stuff like workingset, and so on.

    my @keys = grep(!/workingset/, keys %{$session});
    @keys = grep(!/checkbox/, @keys);
    for(keys %{$session})
      {
        $ARGS{$_} = $session->{$_};
      }
      return %ARGS;
</%perl>
</%def>
<%def .working_set><%args>
$ws
$workingSet
$checkbox
$action
</%args>
<%perl>
my $session = $m->session;
#warn Dumper "PATH",$ENV{PATH};
if($ws eq "clear")
  {
    #warn "clearing working set" if DEBUG;
    $workingSet->clear;

    $session->{workingset} =  $workingSet;
    $session->{working_set} =  $workingSet;
    $action = "view";
  }
elsif($ws eq "add")
  {
    $action = "prev_".$action;
    $workingSet->takeWorkingSetAction($ws,$checkbox) if $ws;
  }
else
  {
    #warn "chckbox", $checkbox;
    #warn "ref", ref $workingSet;

    $workingSet->takeWorkingSetAction($ws,$checkbox) if $ws;
    $action = "view";
  }

  my %new_args= %{$session->{last}} if ref $session->{last} eq "HASH";
  %new_args = (action => $action, ah => 1) unless ref $session->{last} eq "HASH";
        
  delete $new_args{ws};
  delete $new_args{update_ws};
  delete $new_args{checkbox};
  $session->{working_set} = $session->{workingset} = $workingSet;
  return %new_args;
</%perl>
</%def>
<%args>
%ARGS2
</%args>