[Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jan 16 10:23:49 EST 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2732





------- Comment #14 from maj at fortinbras.us  2009-01-16 10:23 EST -------
(From update of attachment 1204)
>Index: HIVQueryHelper.t
>===================================================================
>--- HIVQueryHelper.t	(revision 15375)
>+++ HIVQueryHelper.t	(working copy)
>@@ -15,7 +15,7 @@
> 
> 
> # lanl-schema.xml characteristics as of $Date: 2008-12-11 08:05:24 -0500 (Thu, 11 Dec 2008) $
>-my ($naliases, $nfields, $ntables) = (175, 86, 14);
>+my ($naliases, $nfields, $ntables) = (165, 96, 14);
> my ($Q, $r, $q);
> # object tests
> isa_ok(new HIVSchema(), "HIVSchema");
>@@ -25,7 +25,7 @@
> 
> #HIVSchema tests
> my $tobj;
########### trash the following 2 lines-- sorry bout that
>-ok( $tobj = new HIVSchema(Bio::Root::IO->catfile(qw(Bio DB HIV lanl-schema.xml))), "schema load");
>+ok( $tobj = new HIVSchema(Bio::Root::IO->catfile(qw(c: Perl site lib Bio DB HIV lanl-schema.xml))), "schema load");
> 
> # methods
> can_ok( $tobj, qw (
>@@ -55,14 +55,14 @@
> is( scalar $tobj->tables, $ntables, "tables complete");
> is( scalar $tobj->aliases, $naliases, "aliases complete");
> my ($tbl, $fld, $col, $als);
>-ok( ($fld) = grep /SequenceEntry.SE_id/, $tobj->fields, "test field present");
>+ok( ($fld) = grep /sequenceentry.se_sequence/, $tobj->fields, "test field present");
> ok( $tbl = $tobj->tablepart($fld), "test field syntax ok");
> ok( $col = $tobj->columnpart($fld), "test field syntax ok");
> ok( $als = $tobj->aliases($fld), "test alias by field name");
>-is( $tobj->primarykey($tbl), 'SequenceEntry.SE_id', "correct primary key for SequenceEntry");
>-is( scalar $tobj->foreignkey('AUthor'), 2, "correct number of foreign keys for AUthor");
>-is( $tobj->foreigntable(($tobj->foreignkey('AUthor'))[1]), 'PUBlication', "correct foreign table for AU_PUB_id");
>-is_deeply( {$tobj->ankh('SEQ_SAMple.SSAM_second_receptor')}, {'SEQ_SAMple.SSAM_second_receptor' => {'ankey'=>'coreceptor','antype'=>'Virus'}}, "correct annotation key hash");
>+is( $tobj->primarykey($tbl), 'sequenceentry.se_id', "correct primary key for SequenceEntry");
>+is( scalar $tobj->foreignkey('author'), 2, "correct number of foreign keys for AUthor");
>+is( $tobj->foreigntable(($tobj->foreignkey('author'))[1]), 'publication', "correct foreign table for au_pub_id");
>+is_deeply( {$tobj->ankh('seq_sample.ssam_second_receptor')}, {'seq_sample.ssam_second_receptor' => {'ankey'=>'Coreceptor','antype'=>'Virus'}}, "correct annotation key hash");
> 
> 
> #Query parser tests


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