lib/SGN/Feature/GBrowse2.pm

   1 =head1 NAME
   2
   3 SGN::Feature::GBrowse2 - subclass of L<SGN::Feature::GBrowse> that tweaks the apache conf for GBrowse 2
   4
   5 =cut
   6
   7 package SGN::Feature::GBrowse2;
   8 use Moose;
   9 use namespace::autoclean;
  10 extends 'SGN::Feature::GBrowse';
  11 use Class::Load ':all';
  12 use Bio::Graphics::FeatureFile;
  13
  14 has '_data_sources' => (
  15     is         => 'ro',
  16     isa        => 'HashRef',
  17     traits     => ['Hash'],
  18     lazy_build => 1,
  19     handles => {
  20         data_sources => 'values',
  21         data_source  => 'get',
  22     },
  23    ); sub _build__data_sources {
  24        my $self = shift;
  25
  26        unless( $self->config_master ) {
  27            warn __PACKAGE__.': no master config found, skipping data sources configuration';
  28            return {};
  29        }
  30
  31        my $ds_class =  __PACKAGE__.'::DataSource';
  32        Class::Load::load_class( $ds_class );
  33
  34        my %sources;
  35        foreach my $type ( $self->config_master->configured_types ) {
  36
  37            # absolutify the path from the config file
  38            my $path = $self->config_master->setting( $type => 'path' )
  39                or die "no path configured for [$type] in ".$self->config_master."\n";
  40            $path = Path::Class::File->new( $path );
  41            unless( $path->is_absolute ) {
  42                $path = $self->conf_dir->file( $path );
  43            }
  44
  45            $sources{$type} = $ds_class->new(
  46                ( map {
  47                    $_ => $self->config_master->setting( $type => $_ )
  48                  } $self->config_master->setting( $type )
  49                ),
  50                name    => $type,
  51                path    => $path,
  52                gbrowse => $self,
  53               );
  54        }
  55
  56        return \%sources;
  57    }
  58
  59 has 'config_master' => (
  60     is => 'ro',
  61     lazy_build => 1,
  62    ); sub _build_config_master {
  63
  64        my $master_file = shift->conf_dir->file('GBrowse.conf');
  65        unless( -f $master_file ) {
  66            warn __PACKAGE__.": master conf file $master_file not found";
  67            return;
  68        }
  69
  70        my $ff = Bio::Graphics::FeatureFile->new( -file => "$master_file" );
  71        $ff->safe( 1 ); #< mark the file as safe, so we can use code refs
  72        return $ff;
  73    }
  74
  75 sub fpc_data_sources {
  76     return
  77         sort { my ($ad,$bd) = map $_->description =~ m|(20\d\d)|,$a,$b; $bd <=> $ad }
  78         grep $_->description =~ /FPC/i,
  79         shift->data_sources;
  80 }
  81
  82 # returns a string of apache configuration to be included during
  83 # startup. will be part of plugin role
  84 around apache_conf => sub {
  85     my ( $orig, $self ) = @_;
  86
  87     my $upstream_conf = $self->$orig();
  88
  89     my $static_dir  = $self->static_dir;
  90     my $static_url  = $self->static_url;
  91
  92     my $conf        = $self->conf_dir;
  93     my $cgibin      = $self->cgi_bin;
  94     my $inc         = $self->perl_inc;
  95     my $fcgi_inc    = @$inc ? "DefaultInitEnv PERL5LIB \"".join(':',@$inc).'"' : '';
  96     my $cgi_inc    =  @$inc ? "SetEnv PERL5LIB ".join(':',@$inc) : '';
  97     my $cgi_url     = $self->cgi_url;
  98     my $tmp         = $self->tmp_dir;
  99
 100     my %runmode_conf = (
 101 #       modperl => <<"",
 102 #    Alias /$url_base "$cgibin"
 103 #    <Location /mgb2>
 104 #      SetHandler perl-script
 105 #      PerlResponseHandler ModPerl::Registry
 106 #      PerlOptions +ParseHeaders
 107 #      PerlSetEnv GBROWSE_CONF "$conf"
 108 #    </Location>
 109
 110         fcgi => <<"",
 111   Alias $cgi_url "$cgibin"
 112   <Location $cgi_url>
 113     SetHandler   fcgid-script
 114     Options      ExecCGI
 115   </Location>
 116   DefaultInitEnv GBROWSE_CONF "$conf"
 117   BusyTimeout 360
 118   IPCCommTimeout 300
 119   MaxRequestLen 20971520
 120   $fcgi_inc
 121
 122         cgi => <<"",
 123 ScriptAlias $cgi_url  "$cgibin"
 124 <Directory "$cgibin">
 125   $cgi_inc
 126   SetEnv GBROWSE_CONF "$conf"
 127   Order allow,deny
 128   Allow from all
 129 </Directory>
 130
 131        );
 132
 133     my $runmode_conf = $runmode_conf{ $self->run_mode }
 134         or confess "invalid run mode '".$self->run_mode."'";
 135
 136     return $upstream_conf.<<EOC;
 137 Alias        "$static_url/i/" "$tmp/images/"
 138 Alias        "$static_url"    "$static_dir"
 139
 140 <Location "$static_url">
 141     SetHandler default-handler\n"
 142 </Location>
 143 <Directory "$static_dir">
 144   Options -Indexes -MultiViews +FollowSymLinks
 145   Order allow,deny
 146   Allow from all
 147 </Directory>
 148
 149 $runmode_conf
 150 EOC
 151
 152 };
 153
 154 1;