From 4d7fb252c593d5623b2185d4d2ecf6eb8cd38515 Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Mon, 18 Mar 2013 09:37:38 +0000
Subject: [PATCH] reformatted source with current perltidy settings
---
modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm | 411 ++++++++----------
modules/t/attributeAdaptor.t | 178 +++-----
2 files changed, 238 insertions(+), 351 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
index 8bab776831..9b855af26c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
@@ -1,3 +1,4 @@
+
=head1 LICENSE
Copyright (c) 1999-2012 The European Bioinformatics Institute and
@@ -58,7 +59,6 @@ use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
-
=head2 new
Arg [...] : Superclass args. See Bio::EnsEMBL::DBSQL::BaseAdaptor
@@ -70,13 +70,11 @@ use vars qw(@ISA);
=cut
-
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
-
# cache creation could go here
return $self;
}
@@ -84,234 +82,207 @@ sub new {
use vars '$AUTOLOAD';
sub AUTOLOAD {
- my ($self,@args) = @_;
- my @array_return=();
- my $ref_return = undef;
- $AUTOLOAD =~ /^.*::(\w+_)+(\w+)$/ ;
+ my ($self, @args) = @_;
+ my @array_return = ();
+ my $ref_return = undef;
+ $AUTOLOAD =~ /^.*::(\w+_)+(\w+)$/;
- my $sub = $1;
+ my $sub = $1;
my $type = $2;
+ # print STDERR "AUTO".$AUTOLOAD."\n";
-
-# print STDERR "AUTO".$AUTOLOAD."\n";
-
-# print STDERR "AUTOLOAD reached with call to $sub of type $type\n";
- if($self->can($sub)){
- return $self->$sub($type,@args);
- }
- else{
- warn("In AttribAdaptor cannot call sub $sub$type\n");
+ # print STDERR "AUTOLOAD reached with call to $sub of type $type\n";
+ if ($self->can($sub)) {
+ return $self->$sub($type, @args);
+ } else {
+ warn("In AttribAdaptor cannot call sub $sub$type\n");
}
return undef;
}
-
-
sub store_on_ {
- my $self = shift;
- my $type = shift;
- my $object = shift;
+ my $self = shift;
+ my $type = shift;
+ my $object = shift;
my $attributes = shift;
my $table;
-
my $object_id;
- if($type =~ /[GT][er][na][en]/){
- if (!ref($object)){
- $object_id = $object;
- }
- else {
- $object_id = $object->dbID;
- }
- $table = lc($type);
-# $type = lc($type);
- }
- else{
- if(!ref($object) || !$object->isa('Bio::EnsEMBL::'.$type)) {
- throw("$type argument is required. but you passed $object");
- }
- if($type eq "Slice"){
- $object_id = $object->get_seq_region_id();
- $table = "seq_region";
- $type = "seq_region";
- }
- else{
- if($type eq "MiscFeature"){
- $type = "misc_feature";
- $table = "misc";
- }
- else{
+ if ($type =~ /[GT][er][na][en]/) {
+ if (!ref($object)) {
+ $object_id = $object;
+ } else {
+ $object_id = $object->dbID;
+ }
$table = lc($type);
- }
-
- $object_id = $object->dbID();
- my $db = $self->db();
-
- if(!$object->is_stored($db)) {
- throw("$type is not stored in this database.");
- }
-
- }
- }
- my $sth = $self->prepare( "INSERT into ".$table."_attrib ".
- "SET ".$type."_id = ?, attrib_type_id = ?, ".
- "value = ? " );
+ # $type = lc($type);
+ } else {
+ if (!ref($object) || !$object->isa('Bio::EnsEMBL::' . $type)) {
+ throw("$type argument is required. but you passed $object");
+ }
+ if ($type eq "Slice") {
+ $object_id = $object->get_seq_region_id();
+ $table = "seq_region";
+ $type = "seq_region";
+ } else {
+ if ($type eq "MiscFeature") {
+ $type = "misc_feature";
+ $table = "misc";
+ } else {
+ $table = lc($type);
+ }
+
+ $object_id = $object->dbID();
+ my $db = $self->db();
+
+ if (!$object->is_stored($db)) {
+ throw("$type is not stored in this database.");
+ }
+
+ }
+ } ## end else [ if ($type =~ /[GT][er][na][en]/)]
+ my $sth = $self->prepare("INSERT into " . $table . "_attrib " . "SET " . $type . "_id = ?, attrib_type_id = ?, " . "value = ? ");
my $undef_circular_cache = 0;
- for my $attrib ( @$attributes ) {
- if(!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
- throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
- "argument expected.");
- }
-
-# next if ! $attrib->value;
-
- my $atid = $self->_store_type( $attrib );
- if ((defined $attrib->code) and ($attrib->code eq 'circular_seq')) {
- $undef_circular_cache = 1;
- }
- $sth->bind_param(1,$object_id,SQL_INTEGER);
- $sth->bind_param(2,$atid,SQL_INTEGER);
- $sth->bind_param(3,$attrib->value,SQL_VARCHAR);
- $sth->execute();
+ for my $attrib (@$attributes) {
+ if (!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
+ throw("Reference to list of Bio::EnsEMBL::Attribute objects " . "argument expected.");
+ }
+
+ # next if ! $attrib->value;
+
+ my $atid = $self->_store_type($attrib);
+ if ((defined $attrib->code) and ($attrib->code eq 'circular_seq')) {
+ $undef_circular_cache = 1;
+ }
+ $sth->bind_param(1, $object_id, SQL_INTEGER);
+ $sth->bind_param(2, $atid, SQL_INTEGER);
+ $sth->bind_param(3, $attrib->value, SQL_VARCHAR);
+ $sth->execute();
}
- if($table eq "seq_region") {
- if ($undef_circular_cache) {
- #the slice is circular
- $object->{'circular'} = 1;
- my $slice_adaptor = $object->adaptor();
- #undefine slice adaptor->is_circular and the circular slice cache
- if (defined $slice_adaptor) {
- $slice_adaptor->{'is_circular'} = undef;
- $slice_adaptor->{'circular_sr_id_cache'} = {};
+ if ($table eq "seq_region") {
+ if ($undef_circular_cache) {
+ #the slice is circular
+ $object->{'circular'} = 1;
+ my $slice_adaptor = $object->adaptor();
+ #undefine slice adaptor->is_circular and the circular slice cache
+ if (defined $slice_adaptor) {
+ $slice_adaptor->{'is_circular'} = undef;
+ $slice_adaptor->{'circular_sr_id_cache'} = {};
+ }
}
- }
}
return;
-}
+} ## end sub store_on_
-
-sub remove_from_{
+sub remove_from_ {
my $self = shift;
my $type = shift;
my $object = shift;
my $code = shift;
my $table;
- if(!ref($object) || !$object->isa('Bio::EnsEMBL::'.$type)) {
- throw("$type argument is required or a attrib code. but you passed $object");
+ if (!ref($object) || !$object->isa('Bio::EnsEMBL::' . $type)) {
+ throw("$type argument is required or a attrib code. but you passed $object");
}
my $object_id;
- if($type eq "Slice"){
- $object_id = $object->get_seq_region_id();
- $table = "seq_region";
- $type = "seq_region";
- if ((defined $code) and ($code eq 'circular_seq')) {
- #undefine slice->is_circular, slice adaptor->is_circular and the circular slice cache
- $object->{'circular'} = undef;
- my $slice_adaptor = $object->adaptor();
- if (defined $slice_adaptor) {
- $slice_adaptor->{'is_circular'} = undef;
- $slice_adaptor->{'circular_sr_id_cache'} = {};
+ if ($type eq "Slice") {
+ $object_id = $object->get_seq_region_id();
+ $table = "seq_region";
+ $type = "seq_region";
+ if ((defined $code) and ($code eq 'circular_seq')) {
+ #undefine slice->is_circular, slice adaptor->is_circular and the circular slice cache
+ $object->{'circular'} = undef;
+ my $slice_adaptor = $object->adaptor();
+ if (defined $slice_adaptor) {
+ $slice_adaptor->{'is_circular'} = undef;
+ $slice_adaptor->{'circular_sr_id_cache'} = {};
+ }
+ }
+ } else {
+ if ($type eq "MiscFeature") {
+ $type = "misc_feature";
+ $table = "misc";
+ } else {
+ $table = lc($type);
+ }
+
+ $object_id = $object->dbID();
+ my $db = $self->db();
+
+ if (!$object->is_stored($db)) {
+ throw("$type is not stored in this database.");
}
- }
- }
- else{
- if($type eq "MiscFeature"){
- $type = "misc_feature";
- $table = "misc";
- }
- else{
- $table = lc($type);
- }
-
- $object_id = $object->dbID();
- my $db = $self->db();
-
- if(!$object->is_stored($db)) {
- throw("$type is not stored in this database.");
- }
}
- if(!defined($object_id)) {
- throw("$type must have dbID.");
+ if (!defined($object_id)) {
+ throw("$type must have dbID.");
}
my $sth;
- if(defined($code)){
- $sth = $self->prepare("DELETE a FROM ".$table."_attrib a ,attrib_type at " .
- "WHERE a.attrib_type_id = at.attrib_type_id AND ".
- "a.".$type."_id = ? AND ".
- "at.code like ?");
- $sth->bind_param(1,$object_id,SQL_INTEGER);
- $sth->bind_param(2,$code,SQL_VARCHAR);
- }
- else{
- $sth = $self->prepare("DELETE FROM ".$table."_attrib " .
- "WHERE ".$type."_id = ?");
- $sth->bind_param(1,$object_id,SQL_INTEGER);
+ if (defined($code)) {
+ $sth = $self->prepare("DELETE a FROM " . $table . "_attrib a ,attrib_type at " . "WHERE a.attrib_type_id = at.attrib_type_id AND " . "a." . $type . "_id = ? AND " . "at.code like ?");
+ $sth->bind_param(1, $object_id, SQL_INTEGER);
+ $sth->bind_param(2, $code, SQL_VARCHAR);
+ } else {
+ $sth = $self->prepare("DELETE FROM " . $table . "_attrib " . "WHERE " . $type . "_id = ?");
+ $sth->bind_param(1, $object_id, SQL_INTEGER);
}
$sth->execute();
$sth->finish();
return;
-}
+} ## end sub remove_from_
sub fetch_all {
throw("Use of method fetch_all not supported for attributes");
}
+sub fetch_all_by_ {
+ my $self = shift;
+ my $type = shift;
+ my $object = shift;
+ my $code = shift;
+ my $table = undef;
-
-sub fetch_all_by_{
- my $self = shift;
- my $type = shift;
- my $object = shift;
- my $code = shift;
- my $table =undef;
-
- if (defined($object)){
- if(!ref($object) || !$object->isa('Bio::EnsEMBL::'.$type)) {
- throw("$type argument is required. but you passed $object");
- }
+ if (defined($object)) {
+ if (!ref($object) || !$object->isa('Bio::EnsEMBL::' . $type)) {
+ throw("$type argument is required. but you passed $object");
+ }
}
my $object_id;
- if($type eq "Slice"){
- $object_id = $object->get_seq_region_id() if defined $object;
- $table = "seq_region";
- $type = "seq_region";
- }
- else{
- if($type eq "MiscFeature"){
- $type = "misc_feature";
- $table = "misc";
- }
- else{
- $table = lc($type);
- }
-
- $object_id = $object->dbID() if defined $object;
+ if ($type eq "Slice") {
+ $object_id = $object->get_seq_region_id() if defined $object;
+ $table = "seq_region";
+ $type = "seq_region";
+ } else {
+ if ($type eq "MiscFeature") {
+ $type = "misc_feature";
+ $table = "misc";
+ } else {
+ $table = lc($type);
+ }
+
+ $object_id = $object->dbID() if defined $object;
}
- my $sql = "SELECT at.code, at.name, at.description, t.value " .
- "FROM ".($table||$type)."_attrib t, attrib_type at ".
- "WHERE at.attrib_type_id = t.attrib_type_id ";
+ my $sql = "SELECT at.code, at.name, at.description, t.value " . "FROM " . ($table || $type) . "_attrib t, attrib_type at " . "WHERE at.attrib_type_id = t.attrib_type_id ";
- if(defined($code)){
- $sql .= 'AND at.code like "'.$code.'" ';
+ if (defined($code)) {
+ $sql .= 'AND at.code like "' . $code . '" ';
}
- if(defined($object_id)){
- $sql .= "AND t.".$type."_id = ".$object_id;
+ if (defined($object_id)) {
+ $sql .= "AND t." . $type . "_id = " . $object_id;
}
-
+
my $sth = $self->prepare($sql);
$sth->execute();
@@ -320,14 +291,12 @@ sub fetch_all_by_{
$sth->finish();
return $results;
-
-}
+} ## end sub fetch_all_by_
-sub DESTROY{
+sub DESTROY {
}
-
#
# _id_check
#
@@ -336,94 +305,84 @@ sub DESTROY{
#
sub _id_check {
- my $self = shift;
+ my $self = shift;
my $ensID = shift;
if ($ensID =~ /^\d+$/) {
- return $ensID;
-
- } elsif (ref($ensID) eq 'Bio::EnsEMBL::Gene' or
- ref($ensID) eq 'Bio::EnsEMBL::Transcript' or
- ref($ensID) eq 'Bio::EnsEMBL::Translation') {
+ return $ensID;
+
+ } elsif ( ref($ensID) eq 'Bio::EnsEMBL::Gene'
+ or ref($ensID) eq 'Bio::EnsEMBL::Transcript'
+ or ref($ensID) eq 'Bio::EnsEMBL::Translation')
+ {
- warning("You should pass a dbID rather than an ensembl object to store the attribute on");
+ warning("You should pass a dbID rather than an ensembl object to store the attribute on");
- if ($ensID->dbID) {
- return $ensID->dbID;
- } else {
- throw("Ensembl object ".$ensID->display_id." doesn't have a dbID, can't store attribute");
- }
+ if ($ensID->dbID) {
+ return $ensID->dbID;
+ } else {
+ throw("Ensembl object " . $ensID->display_id . " doesn't have a dbID, can't store attribute");
+ }
} else {
- throw("Invalid dbID");
+ throw("Invalid dbID");
}
-}
-
+} ## end sub _id_check
# _store_type
sub _store_type {
- my $self = shift;
+ my $self = shift;
my $attrib = shift;
- my $sth1 = $self->prepare
- ("INSERT IGNORE INTO attrib_type set code = ?, name = ?, ".
- "description = ?" );
-
+ my $sth1 = $self->prepare("INSERT IGNORE INTO attrib_type set code = ?, name = ?, " . "description = ?");
- $sth1->bind_param(1,$attrib->code,SQL_VARCHAR);
- $sth1->bind_param(2,$attrib->name,SQL_VARCHAR);
- $sth1->bind_param(3,$attrib->description,SQL_LONGVARCHAR);
+ $sth1->bind_param(1, $attrib->code, SQL_VARCHAR);
+ $sth1->bind_param(2, $attrib->name, SQL_VARCHAR);
+ $sth1->bind_param(3, $attrib->description, SQL_LONGVARCHAR);
- my $rows_inserted = $sth1->execute();
+ my $rows_inserted = $sth1->execute();
my $atid = $sth1->{'mysql_insertid'};
- if($rows_inserted == 0) {
- # the insert failed because the code is already stored
- my $sth2 = $self->prepare
- ("SELECT attrib_type_id FROM attrib_type " .
- "WHERE code = ?");
- $sth2->bind_param(1,$attrib->code,SQL_VARCHAR);
- $sth2->execute();
- ($atid) = $sth2->fetchrow_array();
-
- $sth2->finish();
-
- if(!$atid) {
- throw("Could not store or fetch attrib_type code [".$attrib->code."]\n" .
- "Wrong database user/permissions?");
- }
+ if ($rows_inserted == 0) {
+ # the insert failed because the code is already stored
+ my $sth2 = $self->prepare("SELECT attrib_type_id FROM attrib_type " . "WHERE code = ?");
+ $sth2->bind_param(1, $attrib->code, SQL_VARCHAR);
+ $sth2->execute();
+ ($atid) = $sth2->fetchrow_array();
+
+ $sth2->finish();
+
+ if (!$atid) {
+ throw("Could not store or fetch attrib_type code [" . $attrib->code . "]\n" . "Wrong database user/permissions?");
+ }
}
$sth1->finish();
return $atid;
-}
-
+} ## end sub _store_type
sub _obj_from_sth {
my $self = shift;
- my $sth = shift;
+ my $sth = shift;
my ($code, $name, $desc, $value);
$sth->bind_columns(\$code, \$name, \$desc, \$value);
my @results;
- while($sth->fetch()) {
- push @results, Bio::EnsEMBL::Attribute->new_fast
- ( {'code' => $code,
- 'name' => $name,
- 'description' => $desc,
- 'value' => $value} );
+ while ($sth->fetch()) {
+ push @results,
+ Bio::EnsEMBL::Attribute->new_fast({'code' => $code,
+ 'name' => $name,
+ 'description' => $desc,
+ 'value' => $value});
}
return \@results;
}
-
-
-
1;
diff --git a/modules/t/attributeAdaptor.t b/modules/t/attributeAdaptor.t
index 7501dc4876..092a85430c 100644
--- a/modules/t/attributeAdaptor.t
+++ b/modules/t/attributeAdaptor.t
@@ -8,10 +8,9 @@ use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Attribute;
our $verbose = 1;
-our $clean = 0;
+our $clean = 0;
my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
-
# get a core DBAdaptor
my $db = $multi->get_DBAdaptor("core");
@@ -19,7 +18,6 @@ my $slice_adaptor = $db->get_SliceAdaptor();
my $mfa = $db->get_MiscFeatureAdaptor();
my $ga = $db->get_GeneAdaptor();
-
#
# Test get_AttributeAdaptor works
#
@@ -27,21 +25,18 @@ my $aa = $db->get_AttributeAdaptor();
ok($aa && ref($aa) && $aa->isa('Bio::EnsEMBL::DBSQL::AttributeAdaptor'));
-
# hide the contents of the attrib_type, misc_attrib, seq_region_attrib tables
# so we can test storing etc. with a clean slate
$multi->hide('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type', 'gene_attrib');
-
##############
# MiscFeature functionality tests
#
-my $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name',
- -CODE => 'test_code',
- -DESCRIPTION => 'test_desc',
- -VALUE => 'test_value');
-
+my $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name',
+ -CODE => 'test_code',
+ -DESCRIPTION => 'test_desc',
+ -VALUE => 'test_value');
my $mf = $mfa->fetch_by_dbID(1);
$aa->store_on_MiscFeature($mf, [$attrib]);
@@ -49,18 +44,14 @@ $aa->store_on_MiscFeature($mf, [$attrib]);
#
# make sure the misc_attrib table was updated
#
-my $count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM misc_attrib " .
- "WHERE misc_feature_id = 1")->[0]->[0];
+my $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM misc_attrib " . "WHERE misc_feature_id = 1")->[0]->[0];
ok($count == 1);
#
# make sure the attrib_type table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM attrib_type " .
- "WHERE code = 'test_code'")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code'")->[0]->[0];
ok($count == 1);
#
@@ -72,22 +63,21 @@ ok(@attribs == 1);
$attrib = $attribs[0];
-ok($attrib->name eq 'test_name');
-ok($attrib->code eq 'test_code');
+ok($attrib->name eq 'test_name');
+ok($attrib->code eq 'test_code');
ok($attrib->description eq 'test_desc');
-ok($attrib->value eq 'test_value');
+ok($attrib->value eq 'test_value');
-@attribs = @{ $aa->fetch_all_by_MiscFeature() };
+@attribs = @{$aa->fetch_all_by_MiscFeature()};
ok(@attribs == 1);
$attrib = $attribs[0];
-ok($attrib->name eq 'test_name');
-ok($attrib->code eq 'test_code');
+ok($attrib->name eq 'test_name');
+ok($attrib->code eq 'test_code');
ok($attrib->description eq 'test_desc');
-ok($attrib->value eq 'test_value');
-
+ok($attrib->value eq 'test_value');
#
# test the removal of this attribute
@@ -97,9 +87,7 @@ $aa->remove_from_MiscFeature($mf);
#
# make sure the misc_attrib table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM misc_attrib " .
- "WHERE misc_feature_id = 1")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM misc_attrib " . "WHERE misc_feature_id = 1")->[0]->[0];
ok($count == 0);
@@ -109,19 +97,14 @@ ok($count == 0);
@attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
ok(@attribs == 0);
-
-
-
#################
# Slice functionality tests
#
-
-$attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
- -CODE => 'test_code2',
- -DESCRIPTION => 'test_desc2',
- -VALUE => 'test_value2');
-
+$attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
+ -CODE => 'test_code2',
+ -DESCRIPTION => 'test_desc2',
+ -VALUE => 'test_value2');
my $slice = $slice_adaptor->fetch_by_region('chromosome', '20');
@@ -130,18 +113,14 @@ $aa->store_on_Slice($slice, [$attrib]);
#
# make sure the seq_region_attrib table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM seq_region_attrib " .
- "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
ok($count == 1);
#
# make sure the attrib_type table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM attrib_type " .
- "WHERE code = 'test_code2'")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
ok($count == 1);
#
@@ -150,58 +129,45 @@ ok($count == 1);
@attribs = @{$aa->fetch_all_by_Slice($slice)};
ok(@attribs == 1);
-@attribs = @{$aa->fetch_all_by_Slice($slice,"rubbish")};
+@attribs = @{$aa->fetch_all_by_Slice($slice, "rubbish")};
ok(@attribs == 0);
-@attribs = @{$aa->fetch_all_by_Slice($slice,"test_code2")};
+@attribs = @{$aa->fetch_all_by_Slice($slice, "test_code2")};
ok(@attribs == 1);
-@attribs = @{$aa->fetch_all_by_Slice(undef,"test_code2")};
+@attribs = @{$aa->fetch_all_by_Slice(undef, "test_code2")};
ok(@attribs == 1);
-
$attrib = $attribs[0];
-ok($attrib->name eq 'test_name2');
-ok($attrib->code eq 'test_code2');
+ok($attrib->name eq 'test_name2');
+ok($attrib->code eq 'test_code2');
ok($attrib->description eq 'test_desc2');
-ok($attrib->value eq 'test_value2');
-
+ok($attrib->value eq 'test_value2');
#
# test the removal of this attribute with atrrib code
#
-$aa->remove_from_Slice($slice,"junk");
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM seq_region_attrib " .
- "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
+$aa->remove_from_Slice($slice, "junk");
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
ok($count == 1);
-
-
-
#
# test the removal of this attribute
#
-$aa->remove_from_Slice($slice,"test_code2");
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM seq_region_attrib " .
- "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
+$aa->remove_from_Slice($slice, "test_code2");
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
ok($count == 0);
-
-
#
# make sure the attribute is no longer retrievable
#
@attribs = @{$aa->fetch_all_by_Slice($slice)};
ok(@attribs == 0);
-
-
#
# try to add an attribute with an already existing code
#
@@ -209,18 +175,14 @@ $aa->store_on_Slice($slice, [$attrib]);
#
# make sure the seq_region_attrib table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM seq_region_attrib " .
- "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
ok($count == 1);
#
# make sure the attrib_type table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM attrib_type " .
- "WHERE code = 'test_code2'")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
ok($count == 1);
@attribs = @{$aa->fetch_all_by_Slice($slice)};
@@ -230,15 +192,11 @@ ok(@attribs == 1);
@attribs = @{$aa->fetch_all_by_Slice(undef)};
ok(@attribs == 1);
-
-
#
# test the removal of this attribute
#
$aa->remove_from_Slice($slice);
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM seq_region_attrib " .
- "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
ok($count == 0);
@@ -255,17 +213,14 @@ ok($count == 0);
cmp_ok($new_rows, '>', $current_rows, 'Asserting the storage of undefined attributes will always store them');
}
-
#################
# Gene functionality tests
#
-
-$attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
- -CODE => 'test_code2',
- -DESCRIPTION => 'test_desc2',
- -VALUE => 'test_value2');
-
+$attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
+ -CODE => 'test_code2',
+ -DESCRIPTION => 'test_desc2',
+ -VALUE => 'test_value2');
my $gene = $ga->fetch_by_stable_id('ENSG00000171456');
@@ -274,18 +229,14 @@ $aa->store_on_Gene($gene, [$attrib]);
#
# make sure the seq_region_attrib table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM gene_attrib " .
- "WHERE gene_id = ".$gene->dbID())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
ok($count == 1);
#
# make sure the attrib_type table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM attrib_type " .
- "WHERE code = 'test_code2'")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
ok($count == 1);
#
@@ -294,58 +245,45 @@ ok($count == 1);
@attribs = @{$aa->fetch_all_by_Gene($gene)};
ok(@attribs == 1);
-@attribs = @{$aa->fetch_all_by_Gene($gene,"rubbish")};
+@attribs = @{$aa->fetch_all_by_Gene($gene, "rubbish")};
ok(@attribs == 0);
-@attribs = @{$aa->fetch_all_by_Gene($gene,"test_code2")};
+@attribs = @{$aa->fetch_all_by_Gene($gene, "test_code2")};
ok(@attribs == 1);
-@attribs = @{$aa->fetch_all_by_Gene(undef,"test_code2")};
+@attribs = @{$aa->fetch_all_by_Gene(undef, "test_code2")};
ok(@attribs == 1);
-
$attrib = $attribs[0];
-ok($attrib->name eq 'test_name2');
-ok($attrib->code eq 'test_code2');
+ok($attrib->name eq 'test_name2');
+ok($attrib->code eq 'test_code2');
ok($attrib->description eq 'test_desc2');
-ok($attrib->value eq 'test_value2');
-
+ok($attrib->value eq 'test_value2');
#
# test the removal of this attribute with atrrib code
#
-$aa->remove_from_Gene($gene,"junk");
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM gene_attrib " .
- "WHERE gene_id = " . $gene->dbID())->[0]->[0];
+$aa->remove_from_Gene($gene, "junk");
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
ok($count == 1);
-
-
-
#
# test the removal of this attribute
#
-$aa->remove_from_Gene($gene,"test_code2");
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM gene_attrib " .
- "WHERE gene_id = " . $gene->dbID())->[0]->[0];
+$aa->remove_from_Gene($gene, "test_code2");
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
ok($count == 0);
-
-
#
# make sure the attribute is no longer retrievable
#
@attribs = @{$aa->fetch_all_by_Gene($gene)};
ok(@attribs == 0);
-
-
#
# try to add an attribute with an already existing code
#
@@ -353,18 +291,14 @@ $aa->store_on_Gene($gene, [$attrib]);
#
# make sure the seq_region_attrib table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM gene_attrib " .
- "WHERE gene_id = ".$gene->dbID())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
ok($count == 1);
#
# make sure the attrib_type table was updated
#
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM attrib_type " .
- "WHERE code = 'test_code2'")->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
ok($count == 1);
@attribs = @{$aa->fetch_all_by_Gene($gene)};
@@ -374,15 +308,11 @@ ok(@attribs == 1);
@attribs = @{$aa->fetch_all_by_Gene(undef)};
ok(@attribs == 1);
-
-
#
# test the removal of this attribute
#
$aa->remove_from_Gene($gene);
-$count = $db->dbc->db_handle->selectall_arrayref
- ("SELECT count(*) FROM gene_attrib " .
- "WHERE gene_id = " . $gene->dbID())->[0]->[0];
+$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
ok($count == 0);
@@ -399,8 +329,6 @@ ok($count == 0);
cmp_ok($new_rows, '>', $current_rows, 'Asserting the storage of undefined attributes will always store them');
}
-
-
$multi->restore('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type');
done_testing();
--
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