From 9cc34eb72f244e832ae9c4af1d1f1654ab60c989 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 23 Jul 2004 09:57:20 +0000
Subject: [PATCH] updated tests to use centralised ensembl-test framework
---
modules/runtests.pl | 123 ---
...tiTestDB.conf => MultiTestDB.conf.example} | 9 +-
modules/t/MultiTestDB.pm | 705 ------------------
modules/t/MultiTestDB.t | 5 +-
modules/t/README | 39 +-
modules/t/analysis.t | 5 +-
modules/t/archiveStableId.t | 7 +-
modules/t/argument.t | 3 +-
modules/t/assemblyException.t | 7 +-
modules/t/assemblyExceptionFeature.t | 7 +-
modules/t/assemblyMapper.t | 7 +-
modules/t/attribute.t | 5 +-
modules/t/attributeAdaptor.t | 7 +-
modules/t/canonicalDBAdaptor.t | 9 +-
modules/t/chainedAssemblyMapper.t | 7 +-
modules/t/chromosome.t | 7 +-
modules/t/clone.t | 5 +-
modules/t/compressedSequenceAdaptor.t | 7 +-
modules/t/container.t | 1 -
modules/t/coordSystem.t | 3 +-
modules/t/coordSystemAdaptor.t | 7 +-
modules/t/dbConnection.t | 7 +-
modules/t/dbEntries.t | 7 +-
modules/t/densityFeature.t | 9 +-
modules/t/densityFeatureAdaptor.t | 7 +-
modules/t/densityType.t | 7 +-
modules/t/densityTypeAdaptor.t | 7 +-
modules/t/dnaAlignFeatureAdaptor.t | 7 +-
modules/t/dnaDnaAlignFeature.t | 5 +-
modules/t/dnaPepAlignFeature.t | 7 +-
modules/t/easyargv.t | 1 -
modules/t/exception.t | 3 +-
modules/t/exon.t | 7 +-
modules/t/externalFeatureAdaptor.t | 9 +-
modules/t/feature.t | 7 +-
modules/t/featurePair.t | 5 +-
modules/t/gene.t | 7 +-
modules/t/geneview.t | 7 +-
modules/t/intron.t | 7 +-
modules/t/karyotypeBand.t | 3 +-
modules/t/karyotypeBandAdaptor.t | 7 +-
modules/t/mapLocation.t | 7 +-
modules/t/mapper.t | 1 -
modules/t/marker.t | 7 +-
modules/t/markerAdaptor.t | 7 +-
modules/t/markerFeature.t | 7 +-
modules/t/markerFeatureAdaptor.t | 7 +-
modules/t/markerSynonym.t | 3 +-
modules/t/metaContainer.t | 7 +-
modules/t/metaCoordContainer.t | 7 +-
modules/t/miscFeature.t | 5 +-
modules/t/miscFeatureAdaptor.t | 7 +-
modules/t/miscSet.t | 3 +-
modules/t/miscSetAdaptor.t | 7 +-
modules/t/predictionTranscript.t | 19 +-
modules/t/proteinAlignFeatureAdaptor.t | 7 +-
modules/t/proteinFeature.t | 3 +-
modules/t/proteinFeatureAdaptor.t | 7 +-
modules/t/qtl.t | 7 +-
modules/t/rangeRegistry.t | 3 +-
modules/t/rawContig.t | 7 +-
modules/t/rawContigAdaptor.t | 7 +-
modules/t/repeatConsensus.t | 3 +-
modules/t/repeatConsensusAdaptor.t | 7 +-
modules/t/repeatFeature.t | 3 +-
modules/t/repeatFeatureAdaptor.t | 7 +-
modules/t/repeatMaskedSlice.t | 7 +-
modules/t/seqDumper.t | 7 +-
modules/t/seqEdit.t | 3 +-
modules/t/sequenceAdaptor.t | 7 +-
modules/t/simpleFeature.t | 7 +-
modules/t/slice.t | 7 +-
modules/t/sliceAdaptor.t | 7 +-
modules/t/topLevelAssemblyMapper.t | 7 +-
modules/t/transcript.t | 7 +-
modules/t/translation.t | 7 +-
76 files changed, 218 insertions(+), 1104 deletions(-)
delete mode 100755 modules/runtests.pl
rename modules/t/{MultiTestDB.conf => MultiTestDB.conf.example} (56%)
delete mode 100644 modules/t/MultiTestDB.pm
diff --git a/modules/runtests.pl b/modules/runtests.pl
deleted file mode 100755
index 7deb9afe2e..0000000000
--- a/modules/runtests.pl
+++ /dev/null
@@ -1,123 +0,0 @@
-use strict;
-use warnings;
-
-use lib 't';
-
-use Getopt::Std;
-use Test::Harness;
-use MultiTestDB;
-
-use vars qw($opt_l $opt_h);
-
-#read command line options
-&usage unless getopts('lh');
-
-#print usage on '-h' command line option
-if($opt_h) {
- &usage;
- exit;
-}
-
-#list test files on '-l' command line option
-if($opt_l) {
- foreach my $file (map {s{^\./}{}; $_} @{get_all_tests('.', \@ARGV)}) {
- print "$file\n";
- }
- exit;
-}
-
-
-#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)});
-};
-
-&clean;
-
-sub clean {
- #unset env var indicating final cleanup should be performed
- delete $ENV{"RUNTESTS_HARNESS"};
- exit;
-}
-
-=head2 get_all_tests
-
- Arg [1] : string $dir
- the name of the directory retrieve a list of tests from
- Arg [2] : (optional) listref $input_files
- testfiles or directories to retrieve. If not specified all
- ".t" files in $dir are taken.
- Example : @test_files = read_test_dir('t');
- Description: Returns a list of testfiles in the directories specified by
- the @tests argument. The relative path is given as well as
- with the testnames returned. Only files ending with .t are
- returned. Subdirectories are recursively entered and the test
- files returned within them are returned as well.
- Returntype : listref of strings.
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_all_tests {
- my ($dir, $input_files) = @_;
-
- my @files;
- my @out = ();
- local *DIR;
-
- unless(opendir(DIR, $dir)) {
- warn("WARNING: cannot open directory $dir\n");
- return [];
- }
-
- if($input_files && @$input_files) {
- #input files were specified so use them
- @files = @$input_files;
- } else {
- #otherwise use every file in the directory
- @files = readdir DIR;
- }
-
- #filter out CVS files, files beginning with '.' and files ending in ~
- @files = grep !/(^\.)|(^CVS$)|(~$)/, @files;
-
- foreach my $file (@files) {
- $file = "$dir/$file";
-
- if(-d $file) {
- #do a recursive call on directories
- push @out, @{get_all_tests("$file")};
- } elsif ($file =~ /\.t$/) {
- #files ending with a '.t' are considered test files
- unless(-r $file && -f $file) {
- warn("WARNING: cannot read test file $file\n");
- }
- push @out, $file;
- }
- }
-
- closedir DIR;
-
- return \@out;
-}
-
-
-
-sub usage {
- print "usage:\n";
- print "\tlist tests: run_tests.pl -l [<testfiles or dirs> ...]\n";
- print "\trun tests: run_tests.pl [<testfiles or dirs> ...]\n";
-}
-
-
diff --git a/modules/t/MultiTestDB.conf b/modules/t/MultiTestDB.conf.example
similarity index 56%
rename from modules/t/MultiTestDB.conf
rename to modules/t/MultiTestDB.conf.example
index 40d4e03076..71763cc746 100644
--- a/modules/t/MultiTestDB.conf
+++ b/modules/t/MultiTestDB.conf.example
@@ -5,11 +5,14 @@
'pass' => 'ensembl',
'host' => 'ecs1d',
'zip' => 'test_genome.zip',
-
#add a line with the dbname and module
- 'databases' => { 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor'},
+ 'databases' => {
+ 'homo_sapiens' => {'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor'}
+ }
#uncomment to use preloaded databases (useful when doing lots of testing)
-# 'preloaded' => { 'core' => 'mcvicker_new_schema' }
+# ,'preloaded' => {
+# 'homo_sapiens' => {'core' => 'mcvicker_new_schema' }
+# }
}
diff --git a/modules/t/MultiTestDB.pm b/modules/t/MultiTestDB.pm
deleted file mode 100644
index 7bbe143714..0000000000
--- a/modules/t/MultiTestDB.pm
+++ /dev/null
@@ -1,705 +0,0 @@
-
-
-=pod
-
-=head1 NAME - EnsTestDB
-
-=head1 SYNOPSIS
-
-=head1 DESCRIPTION
-
-
-=head1 METHODS
-
-=cut
-
-package MultiTestDB;
-
-use vars qw(%ENV);
-
-use Bio::EnsEMBL::Utils::Exception qw(throw warning);
-
-use strict;
-
-use DBI;
-use Data::Dumper;
-
-
-#homo sapiens is used if no species is specified
-my $DEFAULT_SPECIES = 'homo_sapiens';
-
-#configuration file extension appended onto species name
-my $FROZEN_CONF_EXT = '.MultiTestDB.frozen.conf';
-
-my $CONF_FILE = 'MultiTestDB.conf';
-
-my $DUMP_DIR = 'test-genome-DBs';
-
-sub new {
- my( $pkg, $species ) = @_;
-
- my $self = bless {}, $pkg;
-
- # go and grab the current directory and store it away
- my $curr_dir = $ENV{'PWD'} . "/".__FILE__;
- $curr_dir =~ s/MultiTestDB.pm$//;
-
- $self->curr_dir($curr_dir);
-
- unless($species) {
- $species = $DEFAULT_SPECIES;
- }
-
- $self->species($species);
-
-
- if ( -e $self->curr_dir . $species . $FROZEN_CONF_EXT) {
- $self->load_config;
- }
- else {
- #load the databases and generate the conf hash
- $self->load_databases;
-
- #freeze configuration in a file
- $self->store_config;
- }
-
-
- #generate the db_adaptors from the $self->{'conf'} hash
- $self->create_adaptors;
-
- return $self;
-}
-
-
-#
-# load config into $self->{'conf'} hash
-#
-sub load_config {
- my $self = shift;
-
- my $conf = $self->curr_dir . $self->species . $FROZEN_CONF_EXT;
-
- eval {
- $self->{'conf'} = do $conf; #reads file into $self->{'conf'}
- };
-
- if($@) {
- die("Could not read frozen configuration file '$conf'\n");
- }
-}
-
-
-
-#
-# Store $self->{'config'} hash into a file
-#
-sub store_config {
- my $self = shift;
-
- my $conf = $self->curr_dir . $self->species . $FROZEN_CONF_EXT;
-
- local *FILE;
-
- open(FILE, ">$conf") or die "Could not open config file ".$conf."\n";
-
- my $string = Dumper($self->{'conf'});
-
- #strip off leading '$VAR1 = '
- $string =~ s/^[\$]VAR1\s*=//;
-
- #store config in file
- print FILE $string;
-
- close FILE;
-}
-
-
-
-#create a set of adaptors based on the $self->{'conf'} hash
-sub create_adaptors {
- my $self = shift;
-
- #establish a connection to each of the databases in the configuration
- foreach my $dbtype (keys %{$self->{'conf'}}) {
-
- my $db = $self->{'conf'}->{$dbtype};
- my $adaptor;
- my $module = $db->{'module'};
-
- #try to instantiate an adaptor for this database
- eval {
-
- # require needs /'s rather than colons
- if ( $module =~ /::/ ) {
- $module =~ s/::/\//g;
- }
- require "${module}.pm";
-
- # but switch back for the new instantiation
- $module =~ s/\//::/g;
-
- $adaptor = $module->new(-dbname => $db->{'dbname'},
- -user => $db->{'user'},
- -pass => $db->{'pass'},
- -port => $db->{'port'},
- -host => $db->{'host'},
- -driver => $db->{'driver'});
- };
-
- if ($@) {
- warning("WARNING: Could not instantiate $dbtype DBAdaptor:\n$@");
- } else {
- $self->{'db_adaptors'}->{$dbtype} = $adaptor;
- }
- }
-}
-
-
-
-
-
-sub load_databases {
- my ($self) = shift;
-
- print STDERR "\nTrying to load [$self->{'species'}] databases\n";
-
- #create database from conf and from zip files
- my $db_conf = do $self->curr_dir . $CONF_FILE;
-
- my $port = $db_conf->{'port'};
- my $driver = $db_conf->{'driver'};
- my $host = $db_conf->{'host'};
- my $pass = $db_conf->{'pass'};
- my $user = $db_conf->{'user'};
- my $zip = $db_conf->{'zip'};
-
- #create a config hash which will be frozen to a file
- $self->{'conf'} = {};
-
- #connect to the database
- my $locator = "DBI:".$driver.":host=".$host.";port=".$port;
- my $db = DBI->connect($locator, $user, $pass, {RaiseError => 1});
-
- unless($db) {
- warning("Can't connect to database $locator");
- return;
- }
-
- #only unzip if there are non-preloaded datbases
- UNZIP: foreach my $dbtype (keys %{$db_conf->{'databases'}}) {
- if (( ! exists $db_conf->{'preloaded'}->{$dbtype} ) ||
- ( ! _db_exists( $db, $db_conf->{'preloaded'}{$dbtype}) )) {
- #unzip database files
- $self->unzip_test_dbs($self->curr_dir . $zip);
- last UNZIP;
- }
- }
-
-
- #create a database for each database specified
- foreach my $dbtype (keys %{$db_conf->{'databases'}}) {
- #don't create a database if there is a preloaded one specified
- if (( $db_conf->{'preloaded'}->{$dbtype} ) &&
- ( _db_exists( $db,$db_conf->{'preloaded'}->{$dbtype} ))) {
- #copy the general config into a dbtype specific config
- $self->{'conf'}->{$dbtype} = {};
- %{$self->{'conf'}->{$dbtype}} = %$db_conf;
- $self->{'conf'}->{$dbtype}->{'module'} = $db_conf->{'databases'}->{$dbtype};
-
- # it's not necessary to store the databases and zip bits of info
- delete $self->{'conf'}->{$dbtype}->{'databases'};
- delete $self->{'conf'}->{$dbtype}->{'zip'};
-
-
- #store the temporary database name in the dbtype specific config
- $self->{'conf'}->{$dbtype}->{'dbname'} = $db_conf->{'preloaded'}->{$dbtype};
- $self->{'conf'}->{$dbtype}->{'preloaded'} = 1;
- } else {
-
- $self->{'conf'}->{$dbtype} = {};
- %{$self->{'conf'}->{$dbtype}} = %$db_conf;
- $self->{'conf'}->{$dbtype}->{'module'} = $db_conf->{'databases'}->{$dbtype};
-
- # it's not necessary to store the databases and zip bits of info
- delete $self->{'conf'}->{$dbtype}->{'databases'};
- delete $self->{'conf'}->{$dbtype}->{'zip'};
-
- #create a unique random dbname
- my $dbname = $db_conf->{'preloaded'}->{$dbtype};
- if ( ! defined $dbname ) {
- $dbname = $self->_create_db_name($dbtype);
- delete $self->{'conf'}->{$dbtype}->{'preloaded'};
- } else {
- $self->{'conf'}->{$dbtype}->{'preloaded'} = 1;
- }
-
- #store the temporary database name in the dbtype specific config
- $self->{'conf'}->{$dbtype}->{'dbname'} = $dbname;
-
- print STDERR "\nCreating db $dbname";
-
- unless($db->do("CREATE DATABASE $dbname")) {
- warning("Could not create database [$dbname]");
- return;
- }
-
- #copy the general config into a dbtype specific config
-
- $db->do("use $dbname");
-
- #load the database with data
- my $dir = $self->curr_dir . "$DUMP_DIR/".$self->species."/$dbtype";
- local *DIR;
-
- unless(opendir(DIR, $dir)) {
- warning("could not open dump directory '$dir'");
- return;
- }
-
- my @files = readdir DIR;
-
- local *FILE;
-
- #read in table creat statements from *.sql files and process them with DBI
-
- foreach my $sql_file (grep /\.sql$/, @files) {
-
- $sql_file = "$dir/$sql_file";
-
- unless(-f $sql_file && -r $sql_file) {
- warning("could not read SQL file '$sql_file'\n");
- next;
- }
-
- open(FILE, $sql_file);
-
- my $sql_com ='';
-
- while (<FILE>) {
- next if ( /^#/ ); # ignore comments
- next unless ( /\S/ ); # ignore lines of white spaces
-
- $sql_com .= $_;
- }
- $sql_com =~ s/;$//; # chop off the last ;
-
- $db->do($sql_com);
-
- close FILE;
-
- #import data from the txt files of the same name
- $sql_file =~ /.*\/(.*)\.sql/;
- my $tablename = $1;
-
- (my $txt_file = $sql_file) =~ s/\.sql$/\.txt/;
-
- unless(-f $txt_file && -r $txt_file) {
- warning("could not read data file '$txt_file'\n");
- next;
- }
-
- $db->do( "load data local infile '$txt_file' into table $tablename" );
-
- }
- }
- print STDERR "\n";
- closedir DIR;
-
- }
-
- $db->disconnect;
-
-}
-
-
-sub unzip_test_dbs {
- my ($self, $zipfile) = @_;
-
- if (-e $self->curr_dir . $DUMP_DIR) {
- warning("Test genome dbs already unpacked\n");
- return;
- }
-
- unless($zipfile) {
- throw("zipfile argument is required\n");
- }
-
- unless(-f $zipfile) {
- warning("zipfile could not be found\n");
- return;
- }
-
- # unzip the zip file quietly
-
- system ( "unzip -q $zipfile -d ". $self->curr_dir );
-}
-
-
-
-
-sub get_DBAdaptor {
- my ($self, $type) = @_;
-
- unless($type) {
- die('type arg must be specified\n');
- }
-
- unless($self->{'db_adaptors'}->{$type}) {
- warning("dbadaptor of type $type is not available\n");
- return undef;
- }
-
- return $self->{'db_adaptors'}->{$type};
-}
-
-
-
-=head2 hide
-
- Arg [1] : string $dbtype
- The type of the database containing the hidden table
- Arg [2] : string $table
- The name of the table to hide
- Example : $multi_test_db->hide('core', 'gene', 'transcript', 'exon');
- Description: Hides the contents of specific table(s) in the specified db.
- The table(s) are first renamed and an empty table are created
- in their place by reading the table schema file.
- Returntype : none
- Exceptions : thrown if the adaptor for dbtype is not available
- thrown if both arguments are not defined
- warning if a table is already hidden
- warning if a table cannot be hidden because its schema file
- cannot be read
- Caller : general
-
-=cut
-
-sub hide {
- my ($self, $dbtype, @tables) = @_;
-
- unless($dbtype && @tables) {
- die("dbtype and table args must be defined\n");
- }
-
- my $adaptor = $self->get_DBAdaptor($dbtype);
-
- unless($adaptor) {
- die "adaptor for $dbtype is not available\n";
- }
-
- foreach my $table (@tables) {
-
- if($self->{'conf'}->{$dbtype}->{'hidden'}->{$table}) {
- warning("table '$table' is already hidden and cannot be hidden again\n");
- next;
- }
-
- my $hidden_name = "_hidden_$table";
-
- #copy contents of table into a temp table
-
- my $sth =
- $adaptor->prepare("CREATE TABLE $hidden_name " .
- "SELECT * FROM $table");
-
- $sth->execute();
- $sth->finish();
-
- #delete the contents of the original table
- $sth = $adaptor->prepare("DELETE FROM $table");
- $sth->execute();
- $sth->finish();
-
- #update the hidden table config
- $self->{'conf'}->{$dbtype}->{'hidden'}->{$table} = $hidden_name;
- }
-}
-
-
-
-=head2 restore
-
- Arg [1] : (optional) $dbtype
- The dbtype of the table(s) to be restored. If not specified all
- hidden tables in all the databases are restored.
- Arg [2] : (optional) @tables
- The name(s) of the table to be restored. If not specified all
- hidden tables in the database $dbtype are restored.
- Example : $self->restore('core', 'gene', 'transcript', 'exon');
- Description: Restores a list of hidden tables. The current version of the
- table is discarded and the hidden table is renamed.
- Returntype : none
- Exceptions : thrown if the adaptor for a dbtype cannot be obtained
- Caller : general
-
-=cut
-
-sub restore {
- my ($self, $dbtype, @tables) = @_;
-
- if(!$dbtype) {
- #restore all of the tables in every dbtype
-
- foreach my $dbtype (keys %{$self->{'conf'}}) {
- $self->restore($dbtype);
- }
-
- #lose the hidden table details
- delete $self->{'conf'}->{'hidden'};
-
- return;
- }
-
- my $adaptor = $self->get_DBAdaptor($dbtype);
- unless($adaptor) {
- die "Adaptor for $dbtype is not available";
- }
-
- if(!@tables) {
- #restore all of the tables for this db
- @tables = keys %{$self->{'conf'}->{$dbtype}->{'hidden'}};
- }
-
- foreach my $table (@tables) {
- my $hidden_name = $self->{'conf'}->{$dbtype}->{'hidden'}->{$table};
-
- #delete current contents of table
- my $sth = $adaptor->prepare("delete from $table");
- $sth->execute();
- $sth->finish();
-
- #copy contents of tmp table back into main table
- $sth = $adaptor->prepare("insert into $table " .
- "select * from $hidden_name");
- $sth->execute();
- $sth->finish();
-
- #drop temp table
- $sth = $adaptor->prepare("drop table $hidden_name");
- $sth->execute();
- $sth->finish();
-
- #delete value from hidden table config
- delete $self->{'conf'}->{$dbtype}->{'hidden'}->{$table};
- }
-}
-
-=head2 save
-
- Arg [1] : string $dbtype
- The type of the database containing the hidden/saved table
- Arg [2] : string $table
- The name of the table to save
- Example : $multi_test_db->save('core', 'gene', 'transcript', 'exon');
- Description: Saves the contents of specific table(s) in the specified db.
- The table(s) are first renamed and an empty table are created
- in their place by reading the table schema file. The contents
- of the renamed table(s) are then copied back into the newly
- created tables. The method piggy-backs on the hide method
- and simply adds in the copying/insertion call.
- Returntype : none
- Exceptions : thrown if the adaptor for dbtype is not available
- warning if a table cannot be copied if the hidden table does not
- exist
- Caller : general
-
-=cut
-
-sub save {
- my ($self, $dbtype, @tables) = @_;
-
- # use the hide method to build the basic tables
- $self->hide($dbtype, @tables);
-
- my $adaptor = $self->get_DBAdaptor($dbtype);
-
- unless($adaptor) {
- die "adaptor for $dbtype is not available\n";
- }
-
- my $hidden_name = '';
- foreach my $table (@tables) {
-
- # only do if the hidden table exists
- if($self->{'conf'}->{$dbtype}->{'hidden'}->{$table}) {
-
- $hidden_name = "_hidden_$table";
-
- #copy the data from the hidden table into the new table
- my $sth = $adaptor->prepare("insert into $table " .
- "select * from $hidden_name");
- $sth->execute;
- }
- else {
- warning("hidden table '$hidden_name' does not exist so saving is not possible\n");
- }
- }
-}
-
-
-sub _db_exists {
- my ( $db, $db_name ) = @_;
-
- my $db_names = $db->selectall_arrayref( "show databases" );
- for my $db_name_ref ( @$db_names ) {
- if( $db_name_ref->[0] eq $db_name ) {
- return 1;
- }
- }
-
- return 0;
-}
-
-
-
-sub compare {
- my ($self, $dbtype, $table) = @_;
-
- warning("save method not yet implemented\n");
-
-}
-
-
-sub species {
- my ($self, $species) = @_;
-
- if($species) {
- $self->{'species'} = $species;
- }
-
- return $self->{'species'};
-}
-
-
-
-sub curr_dir {
- my ($self, $cdir) = @_;
-
- if($cdir) {
- $self->{'_curr_dir'} = $cdir;
- }
-
- return $self->{'_curr_dir'};
-}
-
-
-
-sub _create_db_name {
- my( $self, $dbtype ) = @_;
-
- my @t_info = localtime;
-
- my $date = join ( "_", $t_info[3],$t_info[4]+1);
- my $time = join ( "", $t_info[2],$t_info[1],$t_info[0]);
-
- my $species = $self->species;
-
- # create a unique name using host and date / time info
- my $db_name = "_test_db_${species}_${dbtype}_".$ENV{'USER'}."_".$date."_".$time;
-
- return $db_name;
-}
-
-
-
-
-
-sub cleanup {
- my $self = shift;
-
- #delete the unpacked schema and data files
- $self->_delete_files($self->curr_dir . $DUMP_DIR);
-
- #remove all of the handles on dbadaptors
- foreach my $dbtype (keys %{$self->{'db_adaptors'}}) {
- delete $self->{'db_adaptors'}->{$dbtype};
- }
-
- #delete each of the created temporary databases
- foreach my $dbtype (keys %{$self->{'conf'}}) {
-
- my $db_conf = $self->{'conf'}->{$dbtype};
- my $host = $db_conf->{'host'};
- my $user = $db_conf->{'user'};
- my $pass = $db_conf->{'pass'};
- my $port = $db_conf->{'port'};
- my $driver = $db_conf->{'driver'};
- my $dbname = $db_conf->{'dbname'};
-
- if( $db_conf->{'preloaded'} ) {
- next;
- }
- #connect to the database
- my $locator = "DBI:".$driver.":host=".$host.";port=".$port;
-
- my $db = DBI->connect($locator, $user, $pass, {RaiseError => 1});
-
- unless($db) {
- die "Can't connect to database $locator";
- }
-
- print STDERR "Dropping db $dbname \n";
- $db->do("DROP database $dbname");
- $db->disconnect;
- }
-
- my $conf_file = $self->curr_dir . $self->species . $FROZEN_CONF_EXT;
-
- #delete the frozen config file
- if(-e $conf_file && -f $conf_file) {
- unlink $conf_file;
- }
-}
-
-
-sub _delete_files {
- my ($self, $dir) = @_;
-
- local *DIR;
- opendir DIR, $dir;
-
- #ignore files starting with '.'
-
- my @files = grep !/^\./, readdir DIR;
-
- foreach my $file (@files) {
-
- $file = $dir ."/". $file;
- if(-d $file) {
-
- #call recursively on subdirectories
- $self->_delete_files($file);
-
- } else {
- unlink $file;
- }
- }
- closedir DIR;
-
- rmdir $dir;
-}
-
-
-sub DESTROY {
- my( $self ) = shift;
-
- if($ENV{'RUNTESTS_HARNESS'}) {
- #restore tables, do nothing else we want to use the database for
- #the other tests as well
- $self->restore;
- } else {
- #we are runnning a stand-alone test, cleanup created databases
- print STDERR "\nCleaning up....\n";
- #restore database state since we may not actually delete it in the
- #cleanup - it may be defined as a preloaded db
- $self->restore;
- $self->cleanup;
- }
-}
-
-
-
-
-1;
-
diff --git a/modules/t/MultiTestDB.t b/modules/t/MultiTestDB.t
index 70cfe9d5bd..ed88d3b231 100755
--- a/modules/t/MultiTestDB.t
+++ b/modules/t/MultiTestDB.t
@@ -1,16 +1,15 @@
-use lib 't';
use Test;
use strict;
BEGIN { $| = 1; plan tests => 9 }
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
ok(1);
# Database will be dropped when this
# object goes out of scope
-my $ens_test = MultiTestDB->new;
+my $ens_test = Bio::EnsEMBL::Test::MultiTestDB->new;
ok($ens_test);
diff --git a/modules/t/README b/modules/t/README
index 3f50eb9e6a..eff5cdb81e 100755
--- a/modules/t/README
+++ b/modules/t/README
@@ -1,24 +1,35 @@
-This directory contains a set of tests for the EnsEMBL API
+This directory contains a set of tests for the Ensembl API
modules. The test_genome.zip file contains the set of data
that is used by the tests.
-In order to run the tests you must update the MultiTestDB.conf
-file with the information (username, host, etc.) for a mysql
-instance where you have write permission. Running test case(s)
-which require a database will automatically create and remove
-a temporary database during the test(s) execution.
+The test system requires some modules which are in a seperate
+CVS module ensembl-test. To use the tests you must add the
+ensembl-test modules to your PERL5LIB environment variable.
-To run multiple tests at once use the runtests.pl script in
-the modules directory. To run a single test simply execute
-the .t file:
+Example:
+
+setenv PERL5LIB ${PERL5LIB}:${ENSHOME}/ensembl-test/modules
+
+In order to run the tests you must create a t/MultiTestDB.conf
+file with connection details (username, host, etc.) for a mysql
+instance where you have write permission. An example file named
+MultiTestDB.conf.example is included in the /t directory.
+Running test case(s) which require a database will
+automatically create and remove a temporary database during the
+test(s) execution.
+
+To run multiple tests at once use the runtests.pl script
+which is found in the ensembl-test/scripts directory. It
+may be useful to add this directory to your path.
+To run a single test simply execute the .t file:
Examples:
-#run all tests in the t directory
-perl runtests.pl t
+# run all tests in the t directory
+runtests.pl t
-#run 3 tests
-perl runtests.pl t/gene.t t/exon.t t/densityFeature.t
+# run 3 tests
+runtests.pl t/gene.t t/exon.t t/densityFeature.t
-#run a single test
+# run a single test
perl t/gene.t
diff --git a/modules/t/analysis.t b/modules/t/analysis.t
index e42fac8082..51e7465a74 100644
--- a/modules/t/analysis.t
+++ b/modules/t/analysis.t
@@ -1,4 +1,3 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -8,7 +7,7 @@ BEGIN { $| = 1;
my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
our $verbose = 0;
@@ -16,7 +15,7 @@ $loaded = 1;
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok( $multi );
$multi->hide( "core", "analysis" );
diff --git a/modules/t/archiveStableId.t b/modules/t/archiveStableId.t
index 3731d33a4d..3790d2e869 100644
--- a/modules/t/archiveStableId.t
+++ b/modules/t/archiveStableId.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -8,9 +7,9 @@ BEGIN { $| = 1;
plan tests => 9;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
@@ -20,7 +19,7 @@ our $verbose = 0;
#
ok(1);
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
my $asia = $db->get_ArchiveStableIdAdaptor();
diff --git a/modules/t/argument.t b/modules/t/argument.t
index e8fb3eee6a..f0464111d9 100644
--- a/modules/t/argument.t
+++ b/modules/t/argument.t
@@ -1,14 +1,13 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 4;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
diff --git a/modules/t/assemblyException.t b/modules/t/assemblyException.t
index 8a0ae822fc..701f3beb49 100644
--- a/modules/t/assemblyException.t
+++ b/modules/t/assemblyException.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -7,14 +6,14 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DnaDnaAlignFeature;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok(1);
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/assemblyExceptionFeature.t b/modules/t/assemblyExceptionFeature.t
index 6d92666930..78fd352aea 100644
--- a/modules/t/assemblyExceptionFeature.t
+++ b/modules/t/assemblyExceptionFeature.t
@@ -1,20 +1,19 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 9;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::AssemblyExceptionFeature;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
#
diff --git a/modules/t/assemblyMapper.t b/modules/t/assemblyMapper.t
index 244f4d47ec..2e3354a42b 100644
--- a/modules/t/assemblyMapper.t
+++ b/modules/t/assemblyMapper.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,12 +5,12 @@ BEGIN { $| = 1;
plan tests => 9;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
#
diff --git a/modules/t/attribute.t b/modules/t/attribute.t
index 29ef018ab0..2712632d13 100644
--- a/modules/t/attribute.t
+++ b/modules/t/attribute.t
@@ -1,11 +1,10 @@
-use lib 't';
use strict;
use warnings;
use Bio::EnsEMBL::Attribute;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
@@ -14,7 +13,7 @@ BEGIN { $| = 1;
plan tests => 8;
}
-use TestUtils qw( debug test_getter_setter );
+use Bio::EnsEMBL::Test::TestUtils;
#
# test constructor
diff --git a/modules/t/attributeAdaptor.t b/modules/t/attributeAdaptor.t
index 545e8cb9d8..2f5b4f2310 100644
--- a/modules/t/attributeAdaptor.t
+++ b/modules/t/attributeAdaptor.t
@@ -1,19 +1,18 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 22;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Attribute;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
my $db = $multi->get_DBAdaptor("core");
diff --git a/modules/t/canonicalDBAdaptor.t b/modules/t/canonicalDBAdaptor.t
index 0871ce7b4f..4721514081 100644
--- a/modules/t/canonicalDBAdaptor.t
+++ b/modules/t/canonicalDBAdaptor.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -9,15 +8,15 @@ BEGIN { $| = 1;
}
-use TestUtils qw(debug test_getter_setter);
-use MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor;
# Get a DBAdaptor to from the test system
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
ok($multi);
my $db = $multi->get_DBAdaptor("core");
ok($db);
@@ -85,7 +84,7 @@ $test_adaptor = $db->get_MarkerAdaptor();
ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor"));
# Note get_BlastAdaptor() and get_SNPAdaptor() require DBs of type
-# 'blast' and 'lite' respectively - these are not available via MultiTestDB
+# 'blast' and 'lite' respectively - these are not available via Bio::EnsEMBL::Test::MultiTestDB
#my $blast_db = $multi->get_DBAdaptor("lite");
#ok($blast_db);
#$test_adaptor = $blast_db->get_BlastAdaptor();
diff --git a/modules/t/chainedAssemblyMapper.t b/modules/t/chainedAssemblyMapper.t
index 46c421fe13..44612091a1 100644
--- a/modules/t/chainedAssemblyMapper.t
+++ b/modules/t/chainedAssemblyMapper.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,12 +5,12 @@ BEGIN { $| = 1;
plan tests => 14;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
#
diff --git a/modules/t/chromosome.t b/modules/t/chromosome.t
index f8f2687914..9f2caa8fb6 100644
--- a/modules/t/chromosome.t
+++ b/modules/t/chromosome.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -9,8 +8,8 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Utils::Exception qw(verbose);
use Bio::EnsEMBL::Chromosome;
@@ -36,7 +35,7 @@ my $CHR = '20';
my $DBID = 123;
my $LENGTH = 250_000_000;
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
my $ca = $db->get_ChromosomeAdaptor;
diff --git a/modules/t/clone.t b/modules/t/clone.t
index a3b175ddfc..f43fa56546 100644
--- a/modules/t/clone.t
+++ b/modules/t/clone.t
@@ -1,10 +1,9 @@
-use lib 't';
use Test;
use strict;
BEGIN { $| = 1; plan tests => 6;}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::Seq;
use Bio::EnsEMBL::RawContig;
use Bio::EnsEMBL::Clone;
@@ -25,7 +24,7 @@ ok(1);
# Database will be dropped when this
# object goes out of scope
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
ok($multi);
diff --git a/modules/t/compressedSequenceAdaptor.t b/modules/t/compressedSequenceAdaptor.t
index 0cc46276d7..bd65e370d2 100644
--- a/modules/t/compressedSequenceAdaptor.t
+++ b/modules/t/compressedSequenceAdaptor.t
@@ -1,21 +1,20 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 3;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Slice;
our $verbose= 0;
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
#
diff --git a/modules/t/container.t b/modules/t/container.t
index 3643a452da..6f2e74b7e7 100644
--- a/modules/t/container.t
+++ b/modules/t/container.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
diff --git a/modules/t/coordSystem.t b/modules/t/coordSystem.t
index 9176b17d07..fcf1dcb238 100644
--- a/modules/t/coordSystem.t
+++ b/modules/t/coordSystem.t
@@ -1,10 +1,9 @@
use strict;
use warnings;
-use lib 't';
use Bio::EnsEMBL::CoordSystem;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
diff --git a/modules/t/coordSystemAdaptor.t b/modules/t/coordSystemAdaptor.t
index 840ad0d624..bf32f4b297 100644
--- a/modules/t/coordSystemAdaptor.t
+++ b/modules/t/coordSystemAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,12 +5,12 @@ BEGIN { $| = 1;
plan tests => 32;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
diff --git a/modules/t/dbConnection.t b/modules/t/dbConnection.t
index 3ccceb4763..3f7357b03c 100644
--- a/modules/t/dbConnection.t
+++ b/modules/t/dbConnection.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -8,9 +7,9 @@ BEGIN { $| = 1;
plan tests => 30;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::DBSQL::DBConnection;
@@ -21,7 +20,7 @@ our $verbose = 0;
#
ok(1);
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index 65bf9bc617..22f95b066b 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -7,8 +6,8 @@ BEGIN { $| = 1;
plan tests => 42;
}
-use MultiTestDB;
-use TestUtils qw ( debug test_getter_setter count_rows );
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::DBEntry;
@@ -22,7 +21,7 @@ debug( "Startup test" );
#
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
diff --git a/modules/t/densityFeature.t b/modules/t/densityFeature.t
index 35e7e44d56..38788c93e9 100644
--- a/modules/t/densityFeature.t
+++ b/modules/t/densityFeature.t
@@ -1,14 +1,13 @@
-use lib 't';
use strict;
use warnings;
use Bio::EnsEMBL::DensityFeature;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Analysis;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
@@ -20,9 +19,9 @@ BEGIN { $| = 1;
plan tests => 4;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/densityFeatureAdaptor.t b/modules/t/densityFeatureAdaptor.t
index f589e75ad1..2531c6938b 100644
--- a/modules/t/densityFeatureAdaptor.t
+++ b/modules/t/densityFeatureAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -11,8 +10,8 @@ use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::DensityFeature;
-use TestUtils qw( debug );
-use MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Test::MultiTestDB;
BEGIN { $| = 1;
use Test;
@@ -24,7 +23,7 @@ BEGIN { $| = 1;
our $verbose = 0;
verbose('WARNING');
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/densityType.t b/modules/t/densityType.t
index 78732025b7..7c660e894d 100644
--- a/modules/t/densityType.t
+++ b/modules/t/densityType.t
@@ -1,13 +1,12 @@
-use lib 't';
use strict;
use warnings;
use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::Analysis;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
@@ -18,7 +17,7 @@ BEGIN { $| = 1;
plan tests => 9;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
diff --git a/modules/t/densityTypeAdaptor.t b/modules/t/densityTypeAdaptor.t
index 820209eb69..b33c81a7d8 100644
--- a/modules/t/densityTypeAdaptor.t
+++ b/modules/t/densityTypeAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
@@ -7,15 +6,15 @@ BEGIN { $| = 1;
plan tests => 20;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DensityType;
-use TestUtils qw(count_rows);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok( $multi );
my $db = $multi->get_DBAdaptor( "core" );
diff --git a/modules/t/dnaAlignFeatureAdaptor.t b/modules/t/dnaAlignFeatureAdaptor.t
index 293e054c24..bf085052f6 100644
--- a/modules/t/dnaAlignFeatureAdaptor.t
+++ b/modules/t/dnaAlignFeatureAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -7,14 +6,14 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DnaDnaAlignFeature;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok(1);
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/dnaDnaAlignFeature.t b/modules/t/dnaDnaAlignFeature.t
index 64ea7709d8..b326ee3a6b 100644
--- a/modules/t/dnaDnaAlignFeature.t
+++ b/modules/t/dnaDnaAlignFeature.t
@@ -1,5 +1,4 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -8,7 +7,7 @@ BEGIN { $| = 1;
use strict;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::FeaturePair;
@@ -21,7 +20,7 @@ my $CTG_BOUNDARY = 62877;
#
ok(1);
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
diff --git a/modules/t/dnaPepAlignFeature.t b/modules/t/dnaPepAlignFeature.t
index 7ff1a35370..9b760d75ac 100644
--- a/modules/t/dnaPepAlignFeature.t
+++ b/modules/t/dnaPepAlignFeature.t
@@ -1,5 +1,4 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -8,10 +7,10 @@ BEGIN { $| = 1;
use strict;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DnaPepAlignFeature;
-use TestUtils qw ( debug test_getter_setter );
+use Bio::EnsEMBL::Test::TestUtils;
# switch on the debug prints
@@ -25,7 +24,7 @@ my $CTG_BOUNDARY = 62877;
#
ok(1);
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
diff --git a/modules/t/easyargv.t b/modules/t/easyargv.t
index e9407ac2ac..c60171fc20 100644
--- a/modules/t/easyargv.t
+++ b/modules/t/easyargv.t
@@ -1,5 +1,4 @@
use strict;
-use lib 't';
use Test;
BEGIN { $| = 1; plan tests => 1;}
diff --git a/modules/t/exception.t b/modules/t/exception.t
index 373b558fd2..de01c097d8 100644
--- a/modules/t/exception.t
+++ b/modules/t/exception.t
@@ -1,14 +1,13 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 9;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Utils::Exception qw(warning verbose throw info
deprecate stack_trace_dump stack_trace);
diff --git a/modules/t/exon.t b/modules/t/exon.t
index 5ceed8f966..4e0f3e875b 100644
--- a/modules/t/exon.t
+++ b/modules/t/exon.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -9,13 +8,13 @@ BEGIN { $| = 1;
my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter count_rows);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
$loaded = 1;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok(1);
diff --git a/modules/t/externalFeatureAdaptor.t b/modules/t/externalFeatureAdaptor.t
index 8df98199c5..bed97c68c2 100644
--- a/modules/t/externalFeatureAdaptor.t
+++ b/modules/t/externalFeatureAdaptor.t
@@ -2,11 +2,11 @@ use strict;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
package ExternalFF1;
use Bio::EnsEMBL::External::ExternalFeatureAdaptor;
- use MultiTestDB;
+ use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Feature;
use vars qw(@ISA);
@@ -41,7 +41,7 @@ package ExternalFF1;
package ExternalFF2;
use Bio::EnsEMBL::External::ExternalFeatureAdaptor;
- use MultiTestDB;
+ use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Feature;
use vars qw(@ISA);
@@ -77,8 +77,7 @@ package ExternalFF2;
package Test;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
diff --git a/modules/t/feature.t b/modules/t/feature.t
index 59858e1b6f..8a9d9304fe 100644
--- a/modules/t/feature.t
+++ b/modules/t/feature.t
@@ -1,25 +1,24 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 102;
}
-use TestUtils qw( debug test_getter_setter );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::CoordSystem;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
our $verbose= 0; #turn on or off debug statements
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
my $coord_system = Bio::EnsEMBL::CoordSystem->new
diff --git a/modules/t/featurePair.t b/modules/t/featurePair.t
index d367105e2c..e017d049e0 100644
--- a/modules/t/featurePair.t
+++ b/modules/t/featurePair.t
@@ -1,20 +1,19 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 34;
}
-use TestUtils qw( debug test_getter_setter );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::CoordSystem;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
our $verbose= 0; #turn on or off debug statements
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 15bea38266..b45a1d3d03 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -7,8 +6,8 @@ BEGIN { $| = 1;
plan tests => 59;
}
-use MultiTestDB;
-use TestUtils qw ( debug test_getter_setter count_rows);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Transcript;
@@ -22,7 +21,7 @@ our $verbose = 0;
debug( "Startup test" );
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
diff --git a/modules/t/geneview.t b/modules/t/geneview.t
index 7bf01319ff..f662430526 100644
--- a/modules/t/geneview.t
+++ b/modules/t/geneview.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
use vars qw( $verbose );
@@ -9,14 +8,14 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
$verbose = 0;
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok($multi);
diff --git a/modules/t/intron.t b/modules/t/intron.t
index 666a574289..da4bcd7571 100644
--- a/modules/t/intron.t
+++ b/modules/t/intron.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -9,13 +8,13 @@ BEGIN { $| = 1;
my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
$loaded = 1;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok(1);
diff --git a/modules/t/karyotypeBand.t b/modules/t/karyotypeBand.t
index 8bf8e3228c..1639ba1922 100644
--- a/modules/t/karyotypeBand.t
+++ b/modules/t/karyotypeBand.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -9,7 +8,7 @@ BEGIN { $| = 1;
}
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::KaryotypeBand;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::CoordSystem;
diff --git a/modules/t/karyotypeBandAdaptor.t b/modules/t/karyotypeBandAdaptor.t
index 8f6abda114..551d67c8a9 100644
--- a/modules/t/karyotypeBandAdaptor.t
+++ b/modules/t/karyotypeBandAdaptor.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -9,13 +8,13 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::KaryotypeBand;
our $verbose= 0;
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
diff --git a/modules/t/mapLocation.t b/modules/t/mapLocation.t
index 275c780416..8f5129d082 100644
--- a/modules/t/mapLocation.t
+++ b/modules/t/mapLocation.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -7,13 +6,13 @@ BEGIN { $| = 1;
}
use Bio::EnsEMBL::Map::MapLocation;
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
diff --git a/modules/t/mapper.t b/modules/t/mapper.t
index 73cf98c5f2..433d6f2772 100644
--- a/modules/t/mapper.t
+++ b/modules/t/mapper.t
@@ -29,7 +29,6 @@ BEGIN { $| = 1;
use vars qw($loaded); }
END { print "not ok 1\n" unless $loaded; }
-use lib 't';
$loaded = 1;
# $n_test = 0;
diff --git a/modules/t/marker.t b/modules/t/marker.t
index 56a7df40f2..af03817b78 100644
--- a/modules/t/marker.t
+++ b/modules/t/marker.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,14 +5,14 @@ BEGIN { $| = 1;
plan tests => 23;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Map::Marker;
use Bio::EnsEMBL::Map::MarkerSynonym;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
my $dbID = 1;
diff --git a/modules/t/markerAdaptor.t b/modules/t/markerAdaptor.t
index 50d6748b5e..645cce0346 100644
--- a/modules/t/markerAdaptor.t
+++ b/modules/t/markerAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,13 +5,13 @@ BEGIN { $| = 1;
plan tests => 7;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
diff --git a/modules/t/markerFeature.t b/modules/t/markerFeature.t
index 57c99909a7..cd5ab3bad3 100644
--- a/modules/t/markerFeature.t
+++ b/modules/t/markerFeature.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,15 +5,15 @@ BEGIN { $| = 1;
plan tests => 12
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Map::MarkerFeature;
use Bio::EnsEMBL::Map::MarkerSynonym;
use Bio::EnsEMBL::Analysis;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
######
diff --git a/modules/t/markerFeatureAdaptor.t b/modules/t/markerFeatureAdaptor.t
index 73a7334f20..23396dc8bc 100644
--- a/modules/t/markerFeatureAdaptor.t
+++ b/modules/t/markerFeatureAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,12 +5,12 @@ BEGIN { $| = 1;
plan tests => 7
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
######
diff --git a/modules/t/markerSynonym.t b/modules/t/markerSynonym.t
index 2ee5d90b89..cce33ca184 100644
--- a/modules/t/markerSynonym.t
+++ b/modules/t/markerSynonym.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -8,7 +7,7 @@ BEGIN { $| = 1;
use Bio::EnsEMBL::Map::MarkerSynonym;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
diff --git a/modules/t/metaContainer.t b/modules/t/metaContainer.t
index 62a744513b..b7ccb84f1d 100644
--- a/modules/t/metaContainer.t
+++ b/modules/t/metaContainer.t
@@ -1,19 +1,18 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 8;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
-my $mdb = MultiTestDB->new();
+my $mdb = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $mdb->get_DBAdaptor('core');
$mdb->save('core', 'meta');
diff --git a/modules/t/metaCoordContainer.t b/modules/t/metaCoordContainer.t
index a428ee60a3..147718d380 100644
--- a/modules/t/metaCoordContainer.t
+++ b/modules/t/metaCoordContainer.t
@@ -1,19 +1,18 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 7;
}
-use TestUtils qw( debug count_rows);
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor('core');
$multi->save('core', 'meta_coord');
diff --git a/modules/t/miscFeature.t b/modules/t/miscFeature.t
index 52484439ab..6df93a5cc1 100644
--- a/modules/t/miscFeature.t
+++ b/modules/t/miscFeature.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,11 +5,11 @@ BEGIN { $| = 1;
plan tests => 8
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::MiscFeature;
use Bio::EnsEMBL::MiscSet;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
diff --git a/modules/t/miscFeatureAdaptor.t b/modules/t/miscFeatureAdaptor.t
index a223d93980..bdefb8232f 100644
--- a/modules/t/miscFeatureAdaptor.t
+++ b/modules/t/miscFeatureAdaptor.t
@@ -1,14 +1,13 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 18;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::MiscSet;
@@ -16,7 +15,7 @@ use Bio::EnsEMBL::MiscSet;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
my $dba = $multi->get_DBAdaptor("core");
diff --git a/modules/t/miscSet.t b/modules/t/miscSet.t
index 200dcdd977..b76e144a6b 100644
--- a/modules/t/miscSet.t
+++ b/modules/t/miscSet.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -7,7 +6,7 @@ BEGIN { $| = 1;
}
use Bio::EnsEMBL::MiscSet;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
diff --git a/modules/t/miscSetAdaptor.t b/modules/t/miscSetAdaptor.t
index 2f60829abe..a6c6e84492 100644
--- a/modules/t/miscSetAdaptor.t
+++ b/modules/t/miscSetAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,14 +5,14 @@ BEGIN { $| = 1;
plan tests => 21
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::MiscSet;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
diff --git a/modules/t/predictionTranscript.t b/modules/t/predictionTranscript.t
index a779edc352..4b0044a722 100644
--- a/modules/t/predictionTranscript.t
+++ b/modules/t/predictionTranscript.t
@@ -1,15 +1,14 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 39;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::PredictionTranscript;
our $verbose = 0;
@@ -19,7 +18,7 @@ our $verbose = 0;
#
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
@@ -66,30 +65,30 @@ ok($pt->stable_id =~ /.*/ );
#
# 6 test start
#
-ok(&TestUtils::test_getter_setter($pt, 'start', 8));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'start', 8));
#
# 7 test end
#
-ok(&TestUtils::test_getter_setter($pt, 'end', 9));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'end', 9));
#
# 8 test analysis
#
my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name('Vertrna');
-ok(&TestUtils::test_getter_setter($pt, 'analysis', $analysis));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'analysis', $analysis));
#
# 9 test dbID
#
-ok(&TestUtils::test_getter_setter($pt, 'dbID', 11));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'dbID', 11));
#
# 10 test adaptor
#
my $pta = $db->get_PredictionTranscriptAdaptor;
-ok(&TestUtils::test_getter_setter($pt, 'adaptor', $pta));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'adaptor', $pta));
#
# 11-14 test add Exon
@@ -236,7 +235,7 @@ ok($defined_exons_count == $pt->cdna2genomic( 1, $pt->length()));
#
# 30 test type
#
-ok(&TestUtils::test_getter_setter($pt, 'type', 'test'));
+ok(&Bio::EnsEMBL::Test::TestUtils::test_getter_setter($pt, 'type', 'test'));
#
# 31 test fetch_by_stable_id
diff --git a/modules/t/proteinAlignFeatureAdaptor.t b/modules/t/proteinAlignFeatureAdaptor.t
index 558c256e92..40a7ef23c2 100644
--- a/modules/t/proteinAlignFeatureAdaptor.t
+++ b/modules/t/proteinAlignFeatureAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -6,14 +5,14 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::DnaPepAlignFeature;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok(1);
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/proteinFeature.t b/modules/t/proteinFeature.t
index dd333ddcb9..002001cde9 100644
--- a/modules/t/proteinFeature.t
+++ b/modules/t/proteinFeature.t
@@ -1,14 +1,13 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 17;
}
-use TestUtils qw( debug test_getter_setter );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::ProteinFeature;
use Bio::EnsEMBL::Analysis;
diff --git a/modules/t/proteinFeatureAdaptor.t b/modules/t/proteinFeatureAdaptor.t
index 795170d48c..da374564e4 100644
--- a/modules/t/proteinFeatureAdaptor.t
+++ b/modules/t/proteinFeatureAdaptor.t
@@ -1,18 +1,17 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 2;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
my $dba = $multi->get_DBAdaptor("core");
diff --git a/modules/t/qtl.t b/modules/t/qtl.t
index ac9b1b555a..f0930387ae 100644
--- a/modules/t/qtl.t
+++ b/modules/t/qtl.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -7,7 +6,7 @@ BEGIN { $| = 1;
plan tests => 6;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Map::Marker;
use Bio::EnsEMBL::Map::MarkerSynonym;
@@ -15,11 +14,11 @@ use Bio::EnsEMBL::Map::DBSQL::QtlAdaptor;
use Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor;
use Bio::EnsEMBL::Slice;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
my $sa = $db->get_SliceAdaptor();
diff --git a/modules/t/rangeRegistry.t b/modules/t/rangeRegistry.t
index 657560cbb7..6ee3697b91 100644
--- a/modules/t/rangeRegistry.t
+++ b/modules/t/rangeRegistry.t
@@ -1,14 +1,13 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 21;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Mapper::RangeRegistry;
diff --git a/modules/t/rawContig.t b/modules/t/rawContig.t
index 65f37c9d28..ad48a8e7f2 100755
--- a/modules/t/rawContig.t
+++ b/modules/t/rawContig.t
@@ -1,12 +1,11 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 19;
}
-use MultiTestDB;
-use TestUtils qw(debug);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Utils::Exception qw(verbose);
@@ -24,7 +23,7 @@ our $verbose = 0; #set to 1 for debug printing
ok(1);
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
ok($multi);
diff --git a/modules/t/rawContigAdaptor.t b/modules/t/rawContigAdaptor.t
index ab84ac0369..3a8422a297 100644
--- a/modules/t/rawContigAdaptor.t
+++ b/modules/t/rawContigAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -8,10 +7,10 @@ BEGIN { $| = 1;
plan tests => 26;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DBSQL::RawContigAdaptor;
use Bio::EnsEMBL::RawContig;
-use TestUtils qw(test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::Seq;
use Bio::EnsEMBL::Utils::Exception qw(verbose);
@@ -32,7 +31,7 @@ verbose(-1);
#
ok(1);
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/repeatConsensus.t b/modules/t/repeatConsensus.t
index 9b843aca7f..b18db2bbe7 100644
--- a/modules/t/repeatConsensus.t
+++ b/modules/t/repeatConsensus.t
@@ -1,6 +1,5 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::RepeatConsensus;
diff --git a/modules/t/repeatConsensusAdaptor.t b/modules/t/repeatConsensusAdaptor.t
index 52ed37c21b..dd59d46e6d 100644
--- a/modules/t/repeatConsensusAdaptor.t
+++ b/modules/t/repeatConsensusAdaptor.t
@@ -1,8 +1,7 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
BEGIN { $| = 1;
@@ -10,7 +9,7 @@ BEGIN { $| = 1;
plan tests => 24;
}
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
my $verbose = 0;
diff --git a/modules/t/repeatFeature.t b/modules/t/repeatFeature.t
index 6ee22d31c0..a8b5f2e8a5 100644
--- a/modules/t/repeatFeature.t
+++ b/modules/t/repeatFeature.t
@@ -7,7 +7,6 @@ use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::CoordSystem;
use Bio::EnsEMBL::RepeatFeature;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -15,7 +14,7 @@ BEGIN { $| = 1;
}
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
diff --git a/modules/t/repeatFeatureAdaptor.t b/modules/t/repeatFeatureAdaptor.t
index f1ecd5057b..48ef0b7e73 100644
--- a/modules/t/repeatFeatureAdaptor.t
+++ b/modules/t/repeatFeatureAdaptor.t
@@ -1,6 +1,5 @@
use strict;
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -8,13 +7,13 @@ BEGIN { $| = 1;
}
-use MultiTestDB;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
diff --git a/modules/t/repeatMaskedSlice.t b/modules/t/repeatMaskedSlice.t
index ac9f8e14c2..090d77f110 100644
--- a/modules/t/repeatMaskedSlice.t
+++ b/modules/t/repeatMaskedSlice.t
@@ -1,7 +1,6 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
@@ -9,15 +8,15 @@ BEGIN { $| = 1;
plan tests => 6;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::RepeatMaskedSlice;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/seqDumper.t b/modules/t/seqDumper.t
index 1023f63013..fb6cf716fd 100644
--- a/modules/t/seqDumper.t
+++ b/modules/t/seqDumper.t
@@ -1,10 +1,9 @@
-use lib 't';
use strict;
use warnings;
use Bio::EnsEMBL::Utils::SeqDumper;
-use TestUtils qw ( debug test_getter_setter );
-use MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Test::MultiTestDB;
BEGIN { $| = 1;
use Test;
@@ -14,7 +13,7 @@ BEGIN { $| = 1;
our $verbose = 0;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
diff --git a/modules/t/seqEdit.t b/modules/t/seqEdit.t
index 2315ba1420..44b79a792f 100644
--- a/modules/t/seqEdit.t
+++ b/modules/t/seqEdit.t
@@ -1,4 +1,3 @@
-use lib 't';
BEGIN { $| = 1;
use Test;
@@ -7,7 +6,7 @@ BEGIN { $| = 1;
use Bio::EnsEMBL::SeqEdit;
use Bio::EnsEMBL::Attribute;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::TestUtils;
my $code = 'rna edit';
my $desc = 'Post transcriptional RNA edit';
diff --git a/modules/t/sequenceAdaptor.t b/modules/t/sequenceAdaptor.t
index 4c776e3c7a..2f4324d32f 100644
--- a/modules/t/sequenceAdaptor.t
+++ b/modules/t/sequenceAdaptor.t
@@ -1,22 +1,21 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 8;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Slice;
our $verbose= 0;
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
my $CHR = '20';
diff --git a/modules/t/simpleFeature.t b/modules/t/simpleFeature.t
index 918c783a99..2124f87540 100644
--- a/modules/t/simpleFeature.t
+++ b/modules/t/simpleFeature.t
@@ -1,20 +1,19 @@
use strict;
-use lib 't';
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
BEGIN { $| = 1;
use Test;
plan tests => 34;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::SimpleFeature;
our $verbose = 0;
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
# get a core DBAdaptor
#
diff --git a/modules/t/slice.t b/modules/t/slice.t
index 8cdc1418b3..f70419b5fd 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -1,16 +1,15 @@
use strict;
use warnings;
-use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 53;
}
-use TestUtils qw( debug );
+use Bio::EnsEMBL::Test::TestUtils;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::ProjectionSegment;
@@ -28,7 +27,7 @@ my $END = 31_200_000;
my $STRAND = 1;
my $SEQ_REGION_LENGTH = 50e6;
-my $multi_db = MultiTestDB->new;
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi_db->get_DBAdaptor('core');
#
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index 3fa1869572..570cf87de0 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
@@ -8,10 +7,10 @@ BEGIN { $| = 1;
plan tests => 65;
}
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::Slice;
-use TestUtils qw(test_getter_setter debug);
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0;
@@ -22,7 +21,7 @@ my ($CHR, $START, $END, $FLANKING) = ("20", 30_252_000, 31_252_001, 1000);
#
ok(1);
-my $multi = MultiTestDB->new;
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
my $db = $multi->get_DBAdaptor('core');
diff --git a/modules/t/topLevelAssemblyMapper.t b/modules/t/topLevelAssemblyMapper.t
index 95caec343a..0acd0405b6 100644
--- a/modules/t/topLevelAssemblyMapper.t
+++ b/modules/t/topLevelAssemblyMapper.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
BEGIN { $| = 1;
@@ -6,12 +5,12 @@ BEGIN { $| = 1;
plan tests => 7;
}
-use MultiTestDB;
-use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index 4ebb2a7f58..9a95c4100d 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -1,4 +1,3 @@
-use lib 't';
use strict;
use warnings;
use vars qw( $verbose );
@@ -8,13 +7,13 @@ BEGIN { $| = 1;
plan tests => 131;
}
-use MultiTestDB;
-use TestUtils qw( debug test_getter_setter count_rows);
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Intron;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
$verbose = 0; #set to true to turn on debug print outs
diff --git a/modules/t/translation.t b/modules/t/translation.t
index 63e3d7b2da..7ce80be53d 100644
--- a/modules/t/translation.t
+++ b/modules/t/translation.t
@@ -1,8 +1,7 @@
use strict;
use warnings;
-use lib 't';
-use TestUtils qw(debug test_getter_setter count_rows);
+use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Exon;
@@ -17,9 +16,9 @@ END {print "not ok 1\n" unless $loaded;}
#turn on/off debug prints:
our $verbose = 0;
-use MultiTestDB;
+use Bio::EnsEMBL::Test::MultiTestDB;
-my $multi = MultiTestDB->new();
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
$loaded = 1;
--
GitLab