t/LocalDB/Registry.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7         use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 14);
  11
  12         $ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat;t/data/registry/bdb';
  13
  14         use_ok('Bio::DB::Registry');
  15         use_ok('Bio::DB::Flat');
  16 }
  17
  18 # we need a temp directory t/tmp since t/tmp is specified in the registry files
  19 my $tmpdir = File::Spec->catfile(qw(t tmp));
  20 mkdir($tmpdir,0777);
  21
  22 SKIP: {
  23         skip "unable to create temp dir '$tmpdir', skipping tests", 12 unless -d $tmpdir;
  24
  25         my $flat = Bio::DB::Flat->new(-directory  => $tmpdir,
  26                                           -dbname     => 'testflat',
  27                                           -format     => 'fasta',
  28                                           -index      => 'binarysearch',
  29                                                                   -write_flag => 1 );
  30         my $entries = $flat->build_index(test_input_file('cysprot.fa'));
  31         is $entries, 7;
  32
  33         SKIP: {
  34                 test_skip(-tests => 2, -requires_modules => [qw(DB_File)]);
  35
  36                 my $bdb = Bio::DB::Flat->new(-directory  => $tmpdir,
  37                                          -dbname     => 'testbdb',
  38                                          -format     => 'fasta',
  39                                          -index      => 'bdb',
  40                                          -write_flag => 1 );
  41                 ok defined($bdb);
  42                 $entries = $bdb->build_index(test_input_file('cysprot.fa'));
  43                 is $entries, 7;
  44         }
  45
  46         SKIP: {
  47                 test_skip(-tests => 9,
  48                   -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)],
  49                   -requires_networking => 1);
  50
  51                 my $registry = Bio::DB::Registry->new();
  52                 ok defined($registry);
  53                 my @available_services = $registry->services;
  54
  55                 ok grep /testflat/,@available_services;
  56                 my $db = $registry->get_database('testflat');
  57                 ok defined($db);
  58                 my $seq = $db->get_Seq_by_id("ALEU_HORVU");
  59                 ok defined($seq);
  60                 my $sequence = $seq->seq;
  61                 is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
  62
  63                 SKIP: {
  64                         test_skip(-tests => 4, -requires_modules => [qw(DB_File)]);
  65
  66                         ok grep /testbdb/,@available_services;
  67                         $db = $registry->get_database('testbdb');
  68                         ok defined($db);
  69                         $seq = $db->get_Seq_by_id("ALEU_HORVU");
  70                         ok defined($seq);
  71                         $sequence = $seq->seq;
  72                         is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
  73                 }
  74         }
  75 }
  76
  77 END {
  78         File::Path::rmtree($tmpdir) if ($tmpdir && (-d $tmpdir));
  79 }