From ce6b1b316fd07720c8c4ee6e3fc7eaaeda047c4a Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Tue, 12 Nov 2002 15:43:13 +0000
Subject: [PATCH] runtests script now catches SIG, INT and HUP signals to
ensure correct cleanup changed some throws to warnings in MultiTestDB
---
modules/runtests.pl | 16 +++-
modules/t/MultiTestDB.pm | 14 +++-
modules/t/slice.t | 170 ++++++++++++++++++++++++---------------
3 files changed, 127 insertions(+), 73 deletions(-)
diff --git a/modules/runtests.pl b/modules/runtests.pl
index e57cc5a4e4..a987ca6694 100755
--- a/modules/runtests.pl
+++ b/modules/runtests.pl
@@ -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
diff --git a/modules/t/MultiTestDB.pm b/modules/t/MultiTestDB.pm
index 61ec4139be..a153a1603b 100644
--- a/modules/t/MultiTestDB.pm
+++ b/modules/t/MultiTestDB.pm
@@ -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
diff --git a/modules/t/slice.t b/modules/t/slice.t
index 21066492c3..a191ac3ac0 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -1,110 +1,148 @@
+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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