t/RemoteDB/HIV/HIVQuery.t

   1 # testing Bio::DB::Query::HIVQuery
   2 # $Id: HIVQuery.t 232 2008-12-11 14:51:51Z maj $
   3 use strict;
   4 use warnings;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8     test_begin(
   9         -tests => 41,
  10         -requires_modules => [qw(LWP::UserAgent
  11                                  XML::Simple )]
  12     );
  13     use_ok('Bio::DB::Query::HIVQuery');
  14     use_ok('Bio::DB::HIV');
  15     use_ok('Bio::Annotation::Collection');
  16     use_ok('Bio::Annotation::Comment');
  17     use_ok('Bio::Annotation::Reference');
  18     use_ok('Bio::DB::HIV::HIVQueryHelper');
  19
  20 }
  21
  22 my $tobj= new Bio::DB::Query::HIVQuery(-RUN_OPTION=>0);
  23
  24 #object tests
  25 isa_ok($tobj, 'Bio::DB::Query::HIVQuery');
  26
  27 #compliance tests
  28 isa_ok($tobj, 'Bio::Root::Root');
  29 can_ok($tobj, qw( count ids query ));
  30
  31 #methods
  32 can_ok($tobj, qw(
  33                   get_annotations_by_ids
  34                   get_annotations_by_id
  35                   add_annotations_for_id
  36                   remove_annotations_for_ids
  37                   remove_annotations_for_id
  38                   remove_annotations
  39                   get_accessions
  40                   get_accessions_by_ids
  41                   get_accessions_by_id
  42                   )
  43     );
  44 #internals
  45 can_ok($tobj, qw(
  46                   _do_query
  47                   _reset
  48                   _session_id
  49                   _run_option
  50                   add_id
  51                   lanl_base
  52                   map_db
  53                   make_search_if
  54                   search_
  55                   _map_db_uri
  56                   _make_search_if_uri
  57                   _search_uri
  58                   _schema_file
  59                   _schema
  60                   _lanl_query
  61                   _lanl_response
  62                   _create_lanl_query
  63                   _do_lanl_request
  64                   _parse_lanl_response
  65                   _parse_query_string
  66                   _sorry
  67                  )
  68     );
  69
  70 #defaults tests
  71 ok($tobj->_map_db_uri, "_map_db_uri set in default object");
  72 ok($tobj->_make_search_if_uri, "_make_search_if_uri set in default object");
  73 ok($tobj->_search_uri, "_search_uri set in default object");
  74 ok($tobj->_schema_file, "_schema_file set in default object");
  75 ok(defined $tobj->_run_option, "_run_option set in default object");
  76 ok($tobj->{_annotations}, "annotations container available");
  77
  78 # query syntax (no run)
  79 $tobj->_reset;
  80 $tobj->query(['coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any']);
  81 is($tobj->_do_query(0), 0, 'query syntax check 1');
  82 $tobj->_reset;
  83 $tobj->query({'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any'});
  84 is($tobj->_do_query(0), 0, 'query syntax check 2');
  85 $tobj->_reset;
  86 $tobj->query({'query'=>{'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F']}, 'annot'=> ['country']});
  87 is($tobj->_do_query(0),0, 'query syntax check 3');
  88 $tobj->_reset;
  89 $tobj->query("('CCR5 CXCR4', 'CXCR4')[coreceptor] (D F)[subtype] {[country]}");
  90 is($tobj->_do_query(0),0, 'query parser check');
  91
  92 #multiquery parse
  93 $tobj->_reset;
  94 $tobj->query( "(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]");
  95 is($tobj->_do_query(0),0, 'multiquery parse check');
  96
  97 SKIP: {
  98         test_skip(-requires_module => 'HTML::Parser', -tests => 3);
  99         no warnings; # HTML::Parser has an uninited value issue
 100         use_ok('HTML::Parser');
 101         use warnings;
 102         # help test; just tests that file can be written and that tags are in matching
 103         # pairs, with reasonable placement of <html> and </html>
 104         my $hlpf = test_output_file();
 105         my $a = 0;
 106         my $html = 0;
 107         my $h = HTML::Parser->new(empty_element_tags => 1,
 108                                   start_h => [sub {$a++; (shift eq 'html') && ($a==1) && $html++;}, "tagname"],
 109                                   end_h   => [sub {$a--; (shift eq 'html') && ($a==0) && $html++;}, "tagname"] );
 110         ok($tobj->help($hlpf), "help html to file");
 111         {
 112                 local $/;
 113                 undef $/;
 114                 open my $HP, '<', $hlpf or die "Could not read file '$hlpf': $!\n";
 115                 $h->parse(<$HP>);
 116                 is_deeply([$a, $html], [0, 2], "help html parsed");
 117                 close $HP; # Always explicitly close filehandles
 118                 1;
 119         }
 120
 121 }
 122
 123 #exceptions tests
 124 #pre-run query exceptions
 125 $tobj->verbose(2);
 126 $tobj->_reset;
 127 $tobj->query( "narb[scroob]" );
 128 throws_ok {$tobj->_do_query} qr/BadParameter/, "bad field exception check";
 129 $tobj->_reset;
 130 $tobj->query( "narb[phenotype]" );
 131 throws_ok {$tobj->_do_query} qr/BadParameter/, "bad match data exception check";
 132 $tobj->_reset;
 133 $tobj->query( [ 'cd4_count'  => "" ] );
 134 throws_ok {$tobj->_do_query} qr/BadParameter/, "empty field not ok exception check";
 135 $tobj->_reset;
 136 $tobj->{_schema} = undef;
 137 throws_ok {$tobj->_do_query} qr/SchemaNotInit/, "uninitialized schema exception check";
 138 throws_ok {$tobj->count} qr/Query not yet run/, "query not run (level 1) warning check";
 139 throws_ok {$tobj->get_annotations_by_id($tobj->ids)} qr/Requires query run/, "query not run (level 2) warning check";
 140
 141
 142
 143 # network tests
 144 SKIP : {
 145     test_skip(-tests => 10,
 146           -requires_networking => 1);
 147     eval {$tobj  = Bio::DB::Query::HIVQuery->new(-QUERY=>"(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]",-RUN_OPTION=>2)};
 148     if ($@) {
 149         diag($@);
 150         skip("Network problems, skipping all", 10);
 151     }
 152     ok($tobj,"live query");
 153     cmp_ok( $tobj->count, ">=", 12, "enough sequences returned");
 154 # test query object handling of Bio::DB::HIV
 155     my ($tdb, $seqio, $seq);
 156     ok( $tdb = new Bio::DB::HIV, "create Bio::DB::HIV object");
 157         eval {$seqio = $tdb->get_Stream_by_query($tobj)};
 158     if ($@) {
 159         diag($@);
 160         skip("Network problems, skipping all", 7);
 161     }
 162     ok($seqio, "get SeqIO stream from query");
 163 # test HIVAnnotProcessor indirectly
 164     ok($seq = $seqio->next_seq, "access sequence stream");
 165     ok($seq->annotation->get_value('Virus'), "'Virus' annotation present");
 166     like ($seq->annotation->get_value('Virus','phenotype'), qr/SI/, "'Virus' phenotype annotation present");
 167     like ($seq->annotation->get_value('Virus', 'subtype'), qr/[CD]/, "'Virus' subtype annotation present");
 168     ok($seq->accession_number, "GenBank accession available");
 169
 170 # exception checks
 171     $tobj->_reset;
 172     $tobj->verbose(2);
 173     $tobj->query( "2BR02B[accession]" );
 174     throws_ok {$tobj->_do_query(2)} qr/no sequences/i, "no sequences warning check";
 175 }