Skip to content
Snippets Groups Projects
Commit efa7f10a authored by Glenn Proctor's avatar Glenn Proctor
Browse files

Removed irrelevant old test

parent eb0c4e7f
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 0 additions and 325 deletions
modules/t/newtransfer.t deleted 100755 → 0
+ 0
− 325
View file @ eb0c4e7f
## Bioperl Test Harness Script for Modules
##
# CVS Version
# $Id$
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
#-----------------------------------------------------------------------
## perl test harness expects the following output syntax only!
## 1..3
## ok 1 [not ok 1 (if test fails)]
## 2..3
## ok 2 [not ok 2 (if test fails)]
## 3..3
## ok 3 [not ok 3 (if test fails)]
##
## etc. etc. etc. (continue on for each tested function in the .t file)
#-----------------------------------------------------------------------
## We start with some black magic to print on failure.
BEGIN { $| = 1; print "1..43\n";
use vars qw($loaded); }
END {print "not ok 1\n" unless $loaded;
system "rm t/recipient.dump";}
use lib 't';
use EnsTestDB;
$loaded = 1;
print "ok 1\n"; # 1st test passes.
my $ens_donor = EnsTestDB->new();
# Load some data into the db
$ens_donor->do_sql_file("t/donor.dump");
# Get an EnsEMBL db object for the test db
my $fromdb = $ens_donor->get_DBSQL_Obj;
print "ok 2\n";
my $ens_recipient = EnsTestDB->new();
open (TEMP,">t/recipient.dump");
my $meta= "insert into meta (donor_database_locator) values('Bio::EnsEMBL::DBSQL::Obj/host="
.$ens_donor->host.";port=".$ens_donor->port
.";dbname=".$ens_donor->dbname.";user=".$ens_donor->user
.";pass=".$ens_donor->password."')";
print TEMP $meta;
$ens_recipient->do_sql_file("t/recipient.dump");
my $todb = $ens_recipient->get_DBSQL_Obj;
print "ok 3\n";
my @clones = $fromdb->get_Update_Obj->get_updated_Clone_id(1,time());
print "ok 4\n";
foreach my $clone_id (@clones) {
if ($clone_id eq 'AB015355') {
print "ok 5\n";
}
else {
print "not ok 5\n";
print STDERR "unexpected clone id $clone_id\n";
}
my $don_clone=$fromdb->get_Clone($clone_id);
print "ok 6\n";
check_clone($don_clone,7);
$todb->write_Clone($don_clone);
print "ok 15\n";
my $rec_clone=$todb->get_Clone($clone_id);
print "ok 16\n";
check_clone($rec_clone,17);
my $ok;
foreach my $don_gene ($don_clone->get_all_Genes('evidence')) {
if ($don_gene->id =~ /ENSG00000008215|ENSG00000008216|ENSG00000008217/) {
$ok++;
}
push @geneids,$don_gene->id;
if ($don_gene->id eq 'ENSG00000008217') {
check_gene($don_gene,25);
$todb->gene_Obj->write($don_gene);
my $rec_gene=$todb->gene_Obj->get('ENSG00000008217','evidence');
check_gene($rec_gene,31);
}
}
if ($ok == 3) {
print "ok 37\n";
}
else {
print "not ok 37\n";
print STDERR "Got $ok genes instead of 3!\n";
}
foreach my $gene_id (@geneids) {
$fromdb->gene_Obj->delete($gene_id);
}
$don_clone->delete_by_dbID;
print "ok 38\n";
check_delete(39);
}
# end of checks.
sub check_clone {
my ($clone,$c)=@_;
if ($clone->id eq 'AB015355') {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone id not set correctly\n";
}
$c++;
if ($clone->dbID == 1) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone internal_id not set correctly\n";
}
$c++;
if ($clone->version ==2) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone version not set correctly\n";
}
$c++;
if ($clone->embl_id eq 'AB015355') {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone embl_id not set correctly\n";
}
$c++;
if ($clone->embl_version == 1) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone embl_version not set correctly\n";
}
$c++;
if ($clone->htg_phase == 4) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Clone htg_phase not set correctly [",$clone->htg_phase,"]\n";
}
$c++;
if ($clone->created == 932822868) {
print "ok $c\n";
}
else {
print "ok $c\n";
print STDERR "*** SKIPPING Clone created not set correctly ",$clone->created,"\n";
}
$c++;
if ($clone->modified == 961875840) {
print "ok $c\n";
}
else {
print "ok $c\n";
print STDERR "*** SKIPPING Clone modified not set correctly",$clone->modified,"\n";
}
}
sub check_gene {
my ($gene,$c)=@_;
if ($gene->id eq 'ENSG00000008217') {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Gene id not set correctly\n";
}
$c++;
if ($gene->version ==1) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Gene version not set correctly\n";
}
$c++;
foreach my $transcript ($gene->each_Transcript) {
if ($transcript->id eq 'ENST00000009279') {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Transcript id not set correctly\n";
}
$c++;
my $translation=$transcript->translation;
if ($translation->id eq 'ENSP00000009279') {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Transcript id not set correctly\n";
}
$c++;
my $ok=0;
my $suppexon;
foreach $exon ($transcript->each_Exon) {
if( $exon->id eq 'ENSE00000031521' ) {
$suppexon = $exon;
}
if ($exon->id =~ /ENSE00000031517|ENSE00000031518|ENSE00000031519|ENSE00000031520|ENSE00000031521|ENSE00000031522/) {
$ok++;
}
}
if ($ok == 6) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Got $ok exons instead of 6\n";
}
$c++;
my $test =0;
if( defined $suppexon ) {
my @sup = $suppexon->each_Supporting_Feature();
my $sup = shift @sup;
if( defined $sup && $sup->hseqname eq 'AB004857' ) {
$test = 1;
}
}
if( $test == 0 ) {
print STDERR "Supporting feature on exon not retrieved\n";
print "not ok $c\n";
} else {
print "ok $c\n";
}
}
}
sub check_delete {
my ($c)=@_;
my $clone;
eval {
$clone=$fromdb->get_Clone('AB015355');
print STDERR "Clone id " . $clone->dbID . "\n";
};
if ($@) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Bad news, after deleting clone, found " . $clone->id . "\n";
}
$c++;
my $gene;
eval {
$gene=$fromdb->gene_Obj->get('ENSG00000008217');
};
if ($@) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Bad news, after deleting clone, found gene $gene\n";
}
$c++;
my $exon;
eval {
$exon=$fromdb->gene_Obj->get_Exon('ENSE00000031517');
};
if ($@) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Bad news, after deleting clone, found exon $exon\n";
}
$c++;
my $transcript;
eval {
$transcript=$fromdb->gene_Obj->get_Transcript('ENST00000009279');
};
if ($@) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Bad news, after deleting clone, found transcript $transcript\n";
}
$c++;
my $translation;
eval {
$translation=$fromdb->gene_Obj->get_Translation('ENSP00000009279');
};
if ($@) {
print "ok $c\n";
}
else {
print "not ok $c\n";
print STDERR "Bad news, after deleting clone, found translation $translation\n";
}
$c++;
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment