lib/SGN/Feature/GBrowse.pm

   1 =head1 NAME
   2
   3 SGN::Feature::GBrowse - site feature object to provide GBrowse integration
   4
   5 =cut
   6
   7 package SGN::Feature::GBrowse;
   8 use Moose;
   9 use namespace::autoclean;
  10
  11 extends 'SGN::Feature';
  12
  13 use Moose::Util::TypeConstraints;
  14 use MooseX::Types::Path::Class qw | Dir File |;
  15 use MooseX::Types::URI 'Uri';
  16 use HTML::Mason::Interp;
  17
  18 { my $pi = subtype as 'ArrayRef';
  19   coerce $pi,
  20       from 'Value',
  21       via { [$_] };
  22
  23   has 'perl_inc' => ( documentation => 'arrayref of paths to set in PERL5LIB if running in fastcgi or cgi mode',
  24     is => 'ro',
  25     isa => $pi,
  26     default => sub { [] },
  27     coerce => 1,
  28    );
  29 }
  30
  31 has '+description' => (
  32     default => 'Genome browser',
  33    );
  34
  35 has 'conf_dir' => ( documentation => 'directory where GBrowse will look for its conf files',
  36     is => 'ro',
  37     isa => Dir,
  38     coerce => 1,
  39     lazy_build => 1,
  40    ); sub _build_conf_dir { my $self = shift; $self->tmpdir->subdir( 'rendered_conf' ) }
  41
  42 has 'conf_template_dir' => ( documentation => <<'EOD',
  43 directory for configuration templates, which will be rendered on a one-to-one basis into $self->conf_dir during setup()
  44 EOD
  45     is => 'ro',
  46     isa => Dir,
  47     coerce => 1,
  48     lazy_build => 1,
  49    ); sub _build_conf_template_dir { shift->path_to('conf','templates') }
  50
  51 has 'static_url' => ( documentation => 'URL base for GBrowse static files',
  52     is => 'ro',
  53     isa => 'Str',
  54     required => 1,
  55    );
  56
  57 has 'static_dir' => (
  58     is => 'ro',
  59     isa => Dir,
  60     coerce => 1,
  61     required => 1,
  62    );
  63
  64 has 'cgi_url' => (
  65     is => 'ro',
  66     isa => Uri,
  67     required => 1,
  68     coerce => 1,
  69    );
  70 has 'cgi_bin' => (
  71     is => 'ro',
  72     isa => Dir,
  73     coerce => 1,
  74     required => 1,
  75    );
  76
  77 has 'tmp_dir' => (
  78     is => 'ro',
  79     isa => Dir,
  80     coerce => 1,
  81     required => 1,
  82    );
  83
  84 has 'run_mode' => (
  85     is => 'ro',
  86     isa => 'Str',
  87     required => 1,
  88    );
  89
  90
  91 # default database connection info used by gbrowse
  92 has 'default_db_host' => (
  93     is  => 'ro',
  94     isa => 'Str',
  95     lazy_build => 1,
  96    ); sub _build_default_db_host {
  97        my $dsn = shift->context->dbc_profile->{dsn};
  98        return unless $dsn =~ /host=([^;]+)/;
  99        return $1;
 100    }
 101 has 'default_db_user' => (
 102     is  => 'ro',
 103     isa => 'Str',
 104     lazy_build => 1,
 105    ); sub _build_default_db_user {
 106        shift->context->dbc_profile->{user};
 107    }
 108 has 'default_db_password' => (
 109     is  => 'ro',
 110     isa => 'Str',
 111     lazy_build => 1,
 112    ); sub _build_default_db_password {
 113        shift->context->dbc_profile->{password};
 114    }
 115
 116
 117 sub local_inc {
 118     'local @INC = ( '.join(', ',map "'$_'",@INC).' );';
 119 }
 120
 121
 122 # assembles a URI linking to gbrowse.
 123 sub link_uri {
 124     my ( $self, $conf_name, $params ) = @_;
 125
 126     my $uri = URI->new($self->cgi_url."/$conf_name/");
 127     $uri->query_form( %$params );
 128     return $uri;
 129 }
 130
 131
 132 after setup => sub {
 133     my ( $self, $c ) = @_;
 134     $self->render_all_configs;
 135 };
 136
 137 sub xrefs {
 138     my ( $self, $q ) = @_;
 139     return unless defined $q;
 140
 141     # go through each data source and give it a crack at it
 142     return map $_->xrefs($q), $self->data_sources;
 143 }
 144
 145 sub data_sources {
 146     die 'data_sources not yet implemented for gbrowse 1.x';
 147 }
 148
 149
 150 # for each .mas file in the $self->conf_template_dir directory, run
 151 # templating on it and put the output in $self->conf_dir under the
 152 # same filename, without the ending .mas
 153 sub render_all_configs {
 154     my $self = shift;
 155
 156     # all .mas files in the conf_template_dir
 157     my @template_files;
 158     $self->conf_template_dir->recurse(
 159         callback => sub {
 160             my ($child) = @_;
 161             return if $child->is_dir || $child !~ /\.mas$/ || $child =~ /^#/ || $child =~ /~$/;
 162             push @template_files, $child;
 163         });
 164
 165     foreach my $template_file (@template_files) {
 166
 167         # assemble our target filename, which is the same file name
 168         # (minus the .mas), in the $self->conf_dir directory
 169         my $render_target_relative = $template_file->relative( $self->conf_template_dir );
 170         $render_target_relative =~ s/\.mas$//;
 171         my $render_target = $self->conf_dir->file( $render_target_relative );
 172
 173         $render_target->dir->mkpath;
 174         $self->render_config_template( $template_file => $render_target );
 175     }
 176
 177     # also symlink other things in the conf dir into there
 178     for my $conf_thing ( $self->conf_template_dir->parent->children ) {
 179         my $link_target = $self->conf_dir->file( $conf_thing->relative( $conf_thing->parent ) );
 180         unlink $link_target;
 181         symlink $conf_thing, $link_target
 182             or die "$! linking $conf_thing -> $link_target";
 183     }
 184 }
 185
 186 sub render_config_template {
 187     my ( $self, $template_file, $render_target ) = @_;
 188
 189     # render the template into the target file
 190     # my $outbuf;
 191     # my $mason = HTML::Mason::Interp
 192     #     ->new( allow_globals => [qw[ $c $feature ]],
 193     #            autohandler_name => '',
 194     #            comp_root => [['conf_templates', $self->conf_template_dir->stringify ]],
 195     #            out_method => \$outbuf,
 196     #           );
 197     # $mason->set_global( '$c'       => $self->context );
 198     # $mason->set_global( '$feature' => $self          );
 199
 200     # $mason->exec( '/'.$template_file->relative( $self->conf_template_dir) ); #< mason's default search path is current working directory
 201
 202     # $render_target->openw->print( $outbuf );
 203 }
 204
 205 # # returns a string of apache configuration to be included during
 206 # # startup. will be part of plugin role
 207 # sub apache_conf {
 208 #     my ( $self ) = @_;
 209 #     my $dir         = $self->static_dir;
 210 #     my $conf        = $self->conf_dir;
 211 #     my $cgibin      = $self->cgi_bin;
 212 #     my $tmp         = $self->tmp_dir;
 213 #     my $cgiroot     = basename($cgibin);
 214 #     my $perl5lib    = $self->added_to_INC;
 215 #     my $inc         = $perl5lib ? "SetEnv PERL5LIB \"$perl5lib\""   : '';
 216 #     my $fcgi_inc    = $perl5lib ? "-initial-env PERL5LIB=$perl5lib" : '';
 217 #     my $fcgid_inc   = $perl5lib ? "DefaultInitEnv PERL5LIB $perl5lib"        : '';
 218 #     my $modperl_inc = $inc ? "Perl$inc" : '';
 219 #     my $url_base    = $self->url_base;
 220
 221 #     my %runmode_conf = (
 222 #       modperl => <<"",
 223 #    Alias /$url_base "$cgibin"
 224 #    <Location /mgb2>
 225 #      SetHandler perl-script
 226 #      PerlResponseHandler ModPerl::Registry
 227 #      PerlOptions +ParseHeaders
 228 #      PerlSetEnv GBROWSE_CONF "$conf"
 229 #      $modperl_inc
 230 #    </Location>
 231
 232 #       fcgi => <<"",
 233 #   Alias /$url_base "$cgibin"
 234 #   <Location /fgb2>
 235 #     SetHandler   fcgid-script
 236 #     Options      ExecCGI
 237 #   </Location>
 238 #   DefaultInitEnv GBROWSE_CONF $conf
 239 #   $fcgid_inc
 240
 241 #       fastcgi => <<"",
 242 #   Alias /$url_base "$cgibin"
 243 #   <Location /fgb2>
 244 #     SetHandler   fastcgi-script
 245 #     Options      ExecCGI
 246 #   </Location>
 247 #   FastCgiConfig $fcgi_inc -initial-env GBROWSE_CONF=$conf
 248
 249 #       cgi => <<"",
 250 # ScriptAlias  "/$url_base"   "$cgibin"
 251 # <Directory "$cgibin">
 252 #   $inc
 253 #   SetEnv GBROWSE_CONF "$conf"
 254 # </Directory>
 255
 256 #        );
 257
 258 #     my $runmode_conf = $runmode_conf{ $self->run_mode }
 259 #       or confess "invalid run mode '".$self->run_mode."'";
 260
 261 #     return <<EOC;
 262 # Alias        "/$url_base/static/i/" "$tmp/images/"
 263 # Alias        "/$url_base/static"    "$dir"
 264
 265 # <Directory "$dir">
 266 #   Options -Indexes -MultiViews +FollowSymLinks
 267 # </Directory>
 268
 269 # $runmode_conf
 270 # EOC
 271 # }
 272
 273 __PACKAGE__->meta->make_immutable;
 274
 275 1;