lib/SGN/Controller/VigsTool.pm

   1
   2 package SGN::Controller::VigsTool;
   3
   4 use Moose;
   5 use File::Basename;
   6
   7 BEGIN { extends 'Catalyst::Controller'; }
   8
   9 # this function read the database files (Bowtie2) and
  10 # send the list of databases to the view input.mas
  11 sub input :Path('/tools/vigs/')  :Args(0) {
  12         my ($self, $c) = @_;
  13
  14         # get databases path from the configuration file
  15         my $db_path = $c->config->{vigs_db_path};
  16         my $default_db = $c->config->{vigs_default_db};
  17
  18         # get database names from the files in the path
  19         my @databases;
  20         my @tpm_dbs = glob("$db_path/*.rev.1.ebwt");
  21         # my @tpm_dbs = glob("$db_path/*.rev.1.bt2");
  22         foreach my $full_name (@tpm_dbs) {
  23                 push(@databases, basename($full_name, ".rev.1.ebwt"));
  24                 # push(@databases, basename($full_name, ".rev.1.bt2"));
  25         }
  26         # print STDERR "DATABASE ID: ".join(", ", @databases)."\n";
  27
  28         # send the database names to the view file input.mas
  29         $c->stash->{template} = '/tools/vigs/input.mas';
  30         $c->stash->{databases} = \@databases;
  31         $c->stash->{default_db} = $default_db;
  32 }
  33
  34
  35 1;