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Commit ce6b1b31 authored by Graham McVicker's avatar Graham McVicker
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runtests script now catches SIG, INT and HUP signals to ensure correct cleanup 

changed some throws to warnings in MultiTestDB
parent 29389440
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modules/runtests.pl
+ 13
− 3
View file @ ce6b1b31
......@@ -27,19 +27,29 @@ if($opt_l) {
exit;
}
#run all of the specified tests
#set environment var
$ENV{'RUNTESTS_HARNESS'} = 1;
#make sure proper cleanup is done if the user interrupts the tests
$SIG{HUP} = $SIG{KILL} = $SIG{INT} =
sub {warn "\n\nINTERRUPT SIGNAL RECEIEVED\n\n"; &clean;};
#create a multitest db, its destruction will clean up after scripts
my $clean_up = new MultiTestDB;
#run all specified tests
eval {
runtests(@{&get_all_tests('.', \@ARGV)});
};
# do some clean up by creating a MultiTestDB object
&clean;
delete $ENV{"RUNTESTS_HARNESS"};
sub clean {
#unset env var indicating final cleanup should be performed
delete $ENV{"RUNTESTS_HARNESS"};
exit;
}
=head2 get_all_tests
......
modules/t/MultiTestDB.pm
+ 10
− 4
View file @ ce6b1b31
......@@ -184,7 +184,8 @@ sub load_databases {
my $db = DBI->connect($locator, $user, $pass, {RaiseError => 1});
unless($db) {
$self->throw("Can't connect to database $locator");
$self->warn("Can't connect to database $locator");
return;
}
#create a database for each database specified
......@@ -195,7 +196,8 @@ sub load_databases {
print STDERR "\nCreating db $dbname";
unless($db->do("CREATE DATABASE $dbname")) {
$self->throw("Could not create database [$dbname]");
$self->warn("Could not create database [$dbname]");
return;
}
#copy the general config into a dbtype specific config
......@@ -217,7 +219,10 @@ sub load_databases {
my $dir = $self->curr_dir . "$DUMP_DIR/".$self->species."/$dbtype";
local *DIR;
opendir(DIR, $dir) or die "could not open dump directory '$dir'";
unless(opendir(DIR, $dir)) {
$self->warn("could not open dump directory '$dir'");
return;
}
my @files = readdir DIR;
......@@ -286,7 +291,8 @@ sub unzip_test_dbs {
}
unless(-f $zipfile) {
$self->throw("zipfile could not be found\n");
$self->warn("zipfile could not be found\n");
return;
}
# unzip the zip file quietly
......
modules/t/slice.t
+ 104
− 66
View file @ ce6b1b31
use strict;
use warnings;
use lib 't';
use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 4;
plan tests => 27;
}
my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}
use EnsTestDB;
use MultiTestDB;
use Bio::EnsEMBL::DBLoader;
use Bio::EnsEMBL::Slice;
$loaded = 1;
#
#1 TEST - Slice Compiles
#
ok(1);
ok(1);
# Database will be dropped when this
# object goes out of scope
my $ens_test = EnsTestDB->new;
my $CHR = '20';
my $START = 31_000_000;
my $END = 31_200_000;
my $STRAND = 1;
my $ASSEMBLY_TYPE = 'NCBI_30';
my $DBID = 123;
$ens_test->do_sql_file("t/minidatabase.dump");
my $multi_db = MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
ok($ens_test);
#
#2-5 TEST - Slice creation from adaptor
#
my $slice_adaptor = $db->get_SliceAdaptor;
my $slice = $slice_adaptor->fetch_by_chr_start_end($CHR, $START, $END);
ok($slice->chr_name eq $CHR);
ok($slice->chr_start == $START);
ok($slice->chr_end == $END);
ok($slice->adaptor);
my $db = $ens_test->get_DBSQL_Obj;
$sla= $db->get_SliceAdaptor();
$slice = $sla->new_slice('1',4,400,'NCBI_28');
#
#6 TEST - Slice::new (empty)
#
$slice = new Bio::EnsEMBL::Slice(-empty => 1);
ok($slice);
&write_feature();
ok(1);
#
#7-12 TEST - Slice::new
#
$slice = new Bio::EnsEMBL::Slice(-chr_name => $CHR,
-chr_start => $START,
-chr_end => $END,
-strand => $STRAND,
-assembly_type => $ASSEMBLY_TYPE,
-dbid => $DBID);
($outf) = $slice->get_all_SimilarityFeatures_above_score(5);
#ok($outf);
ok($slice->chr_name eq $CHR);
ok($slice->chr_start == $START);
ok($slice->chr_end == $END);
ok($slice->strand == $STRAND);
ok($slice->assembly_type eq $ASSEMBLY_TYPE);
ok($slice->dbID == $DBID);
#
#13 Test - Slice::adaptor
#
$slice->adaptor($slice_adaptor);
ok($slice->adaptor == $slice_adaptor);
sub write_feature {
#
#14 Test - Slice::dbID
#
$slice->dbID(10);
ok($slice->dbID==10);
$dna_f_ad = $db->get_DnaAlignFeatureAdaptor();
#
#15-17 Test Slice::name
#
#verify that chr_name start and end are contained in the name
my $name = $slice->name;
ok($name =~/$CHR/);
ok($name =~/$START/);
ok($name =~/$END/);
#
#18 Test Slice::id
#
ok($slice->id eq $slice->name);
$feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start(5);
$feature1->end (7);
$feature1->strand(1);
$feature1->score(10);
$feature1->seqname(1);
#$feature1->analysis($self->analysis);
#
#19 Test Slice::length
#
ok($slice->length == ($END-$START + 1));
$feature2 = new Bio::EnsEMBL::SeqFeature();
$feature2->start (105);
$feature2->end (107);
$feature2->strand (1);
$feature2->score (10);
$feature2->seqname("dummy-hid");
$fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
-feature2 => $feature2);
#
#20-22 Test Slice::invert
#
my $inverted_slice = $slice->invert;
ok($slice != $inverted_slice); #slice is not same object as inverted slice
#inverted slice on opposite strand
ok($slice->strand == ($inverted_slice->strand * -1));
#slice still on same strand
ok($slice->strand == $STRAND);
push(@feats,$fp);
#
# 23-24 Test Slice::seq
#
my $seq = $slice->seq;
my $invert_seq = $slice->invert->seq;
$feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start(10);
$feature1->end (14);
$feature1->strand(1);
$feature1->score(10);
$feature1->seqname(1);
print STDERR "SEQ=[$seq]\n";
#$feature1->analysis($self->analysis);
ok(length($seq) == $slice->length); #sequence is correct length
print STDERR "[".length($seq)."] != [".$slice->length."]\n";
$seq = uc reverse $seq; #reverse complement seq
$seq =~ s/ACTG/TGAC/g;
ok($seq eq $invert_seq); #revcom same as seq on inverted slice
$feature2 = new Bio::EnsEMBL::SeqFeature();
$feature2->start (106);
$feature2->end (110);
$feature2->strand (1);
$feature2->score (10);
$feature2->seqname('dummy-hid');
#
# 25-26 Test Slice::subseq
#
my $SPAN = 10;
my $sub_seq = $slice->subseq(-$SPAN,$SPAN);
my $invert_sub_seq = $slice->invert->subseq($slice->length + $SPAN,
$slice->length - $SPAN);
ok(length $sub_seq == (2*$SPAN) + 1 );
$seq = uc reverse $seq;
$seq =~ s/ACTG/TGAC/g;
ok($seq eq $invert_seq);
$fp2 = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
-feature2 => $feature2);
push(@feats,$fp2);
$dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new( -features => \@feats );
$dnaf->seqname(1);
$dnaf->hseqname('dummy-hid');
$dnaf->analysis($db->get_AnalysisAdaptor->fetch_by_logic_name("dummy-blast"));
$dna_f_ad->store(1,$dnaf);
}
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