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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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t/Registry.t
1
 
##-*-Perl-*-
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# $Id: Registry.t,v 1.10.6.2 2006/11/30 09:24:00 sendu Exp $
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# test for Bio::DB::Registry, Flat::BinarySearch, and Flat::BDB
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# written by Brian Osborne
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use strict;
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use vars qw($NUMTESTS $old_search_path $no_DB_File $no_LWP $DEBUG);
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use File::Spec;
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BEGIN {
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        $DEBUG = $ENV{BIOPERLDEBUG} || 0;
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        eval { require Test; };
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        if( $@ ) {
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                use lib 't';
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        }
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        use Test;
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        $no_DB_File = 0;
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        $old_search_path = $ENV{OBDA_SEARCH_PATH} if defined $ENV{OBDA_SEARCH_PATH};
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        $ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat;t/data/registry/bdb';
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        eval { require DB_File;
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                         require BerkeleyDB;
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                 };
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        if ($@) {
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                $ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat';
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                $no_DB_File = 1;
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        }
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        eval { require LWP::UserAgent;
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                         require HTTP::Request::Common; };
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        if( $@ ) {
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                $no_LWP =1;
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        }
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        plan tests => ($NUMTESTS=13);
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}
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require Bio::DB::Registry;
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use Bio::DB::Flat;
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use Bio::Root::IO;
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my $tmpdir = File::Spec->catfile(qw(t tmp));
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mkdir($tmpdir,0777);
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ok (-d $tmpdir);
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my $flat = Bio::DB::Flat->new(-directory  => $tmpdir,
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                              -dbname     => 'testflat',
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                              -format     => 'fasta',
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                              -index      => 'binarysearch',
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                              -write_flag => 1 );
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my $entries = $flat->build_index(File::Spec->catfile(qw(t data cysprot.fa)));
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ok $entries == 7;
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if ($no_DB_File){
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    for (1..2) {
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        skip("DB_File or BerkeleyDB not found, skipping DB_File tests",1);
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    }
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} else {
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    my $bdb = Bio::DB::Flat->new(-directory  => $tmpdir,
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                                 -dbname     => 'testbdb',
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                                 -format     => 'fasta',
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                                 -index      => 'bdb',
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                                 -write_flag => 1 );
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    ok defined($bdb);
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    $entries = $bdb->build_index(File::Spec->catfile(qw(t data cysprot.fa)));
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    ok $entries == 7;
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}
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if( $no_LWP ) {
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    for (1..9 ) {
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        skip("No LWP::UserAgent or HTTP::Request::Common modules installed skipping tests",1);
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    }
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} else {
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    my $registry = Bio::DB::Registry->new;
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    ok defined($registry);
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    my @available_services = $registry->services;
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    ok grep /testflat/,@available_services;
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    my $db = $registry->get_database('testflat');
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    ok defined($db);
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    my $seq = $db->get_Seq_by_id("ALEU_HORVU");
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    ok defined($seq);
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    my $sequence = $seq->seq;
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    ok $sequence eq "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
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    if ($no_DB_File) {
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        for (1..4) {
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            skip("DB_File or BerkeleyDB not found, skipping DB_File tests",1);
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        }
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    } else {
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        ok grep /testbdb/,@available_services;
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        $db = $registry->get_database('testbdb');
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        ok defined($db);
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        $seq = $db->get_Seq_by_id("ALEU_HORVU");
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        ok defined($seq);
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        $sequence = $seq->seq;
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        ok $sequence eq "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
96
 
    }
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}
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END {
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        cleanup();
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}
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sub cleanup {
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        eval {
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                Bio::Root::IO->rmtree($tmpdir) if (-d $tmpdir);
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        };
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}
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__END__