diff --git a/modules/t/newtransfer.t b/modules/t/newtransfer.t
deleted file mode 100755
index f7d8fb050dd6590dd0fcd4d0f67665f22bf2a843..0000000000000000000000000000000000000000
--- a/modules/t/newtransfer.t
+++ /dev/null
@@ -1,325 +0,0 @@
-## 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++;
-}
-
-
-
-