diff --git a/misc-scripts/frameshift_transcript_attribs.pl b/misc-scripts/frameshift_transcript_attribs.pl
index 2eb599229619f22cd3a018e4520106bf5120e724..d1805c073aa4c58009efde6a167debcf4a6b421b 100644
--- a/misc-scripts/frameshift_transcript_attribs.pl
+++ b/misc-scripts/frameshift_transcript_attribs.pl
@@ -96,7 +96,7 @@ for my $dbname ( @dbnames ) {
my $transcript = $transcript_adaptor->fetch_by_dbID($transcript_id);
- $attribute_adaptor->store_on_Transcript($transcript, \@attribs) if (!$nostore);
+ $attribute_adaptor->store_on_Transcript($transcript->dbID, \@attribs) if (!$nostore);
print join("\t", $stable_id, $start, $end, $strand, $intron_length, $seq_region_name, "\n") if ($locations);
diff --git a/misc-scripts/surgery/shortintrons2frameshifts.pl b/misc-scripts/surgery/shortintrons2frameshifts.pl
index 5e5e25c4785b12515874f1d0ad2f611e57f3e70c..c8a0178d8d66dcf422d9e9f4b87b456a7f3e1ea2 100644
--- a/misc-scripts/surgery/shortintrons2frameshifts.pl
+++ b/misc-scripts/surgery/shortintrons2frameshifts.pl
@@ -165,7 +165,7 @@ foreach my $gene_id (@gene_ids) {
-START => $cdna_start,
-END => $cdna_start + $fs->length() - 1,
-ALT_SEQ => '');
- $aa->store_on_Transcript($tr, [$seqed->get_Attribute]);
+ $aa->store_on_Transcript($tr->dbID, [$seqed->get_Attribute]);
# adjust cdna coordinates for frameshifted basepairs
if($tr->translation) {
diff --git a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
index 89e3a1581b7eb0e39022b0f0e03de45a7718181f..d1800be2aea40f346e000815ff323e799e3f8192 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
@@ -414,14 +414,13 @@ sub store_on_MiscFeature {
=head2 store_on_Gene
- Arg [1] : Bio::EnsEMBL::Gene $gene
+ Arg [1] : Int $gene_id - the dbID of the gene to store the attributes for
Arg [2] : listref Bio::EnsEMBL::Attribute $attribs
Example : $attribute_adaptor->store_on_Gene($my_gene, $attributes)
Description: Stores all the attributes on the Gene.
Will duplicate things if called twice.
Returntype : none
Exceptions : throw on incorrect arguments
- throw if provided Gene is not stored in this database
Caller : general, GeneAdaptor
Status : Stable
@@ -429,25 +428,16 @@ sub store_on_MiscFeature {
sub store_on_Gene {
my $self = shift;
- my $gene = shift;
+ my $gene_id = shift;
my $attributes = shift;
- if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
- throw("Gene argument expected");
- }
+ my $gene_dbID = $self->_id_check($gene_id);
if(ref($attributes) ne 'ARRAY') {
throw("Reference to list of Bio::EnsEMBL::Attribute objects argument " .
"expected");
}
- my $db = $self->db();
- if(!$gene->is_stored($db)) {
- throw("Gene is not stored in this DB - cannot store attributes.");
- }
-
- my $gene_id = $gene->dbID();
-
my $sth = $self->prepare( "INSERT into gene_attrib ".
"SET gene_id = ?, attrib_type_id = ?, ".
"value = ? " );
@@ -457,8 +447,8 @@ sub store_on_Gene {
throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
"argument expected.");
}
- my $atid = $self->_store_type( $attrib );
- $sth->execute( $gene_id, $atid, $attrib->value() );
+ my $atid = $self->_store_type($attrib);
+ $sth->execute($gene_dbID, $atid, $attrib->value);
}
return;
@@ -467,54 +457,44 @@ sub store_on_Gene {
=head2 store_on_Transcript
- Arg [1] : Bio::EnsEMBL::Transcript $transcript
+ Arg [1] : Int $trans_id
+ The dbID of the transcript to store the attributes for
Arg [2] : listref Bio::EnsEMBL::Attribute $attribs
- Example : $attribute_adaptor->store_on_Transcript($my_transcript,
- $attributes)
+ Example : $attribute_adaptor->store_on_Transcript($trans_id, $attributes)
Description: Stores all the attributes on the Transcript.
Will duplicate things if called twice.
Returntype : none
Exceptions : throw on incorrect arguments
- throw if provided Transcript is not stored in this database
Caller : general, TranscriptAdaptor
Status : Stable
=cut
sub store_on_Transcript {
- my $self = shift;
- my $transcript = shift;
+ my $self = shift;
+ my $trans_id = shift;
my $attributes = shift;
- if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
- throw("Transcript argument expected");
- }
-
- if(ref($attributes) ne 'ARRAY') {
+ my $trans_dbID = $self->_id_check($trans_id);
+
+ if (ref($attributes) ne 'ARRAY') {
throw("Reference to list of Bio::EnsEMBL::Attribute objects argument " .
"expected");
}
- my $db = $self->db();
- if(!$transcript->is_stored($db)) {
- throw("Transcript is not stored in this DB - cannot store attributes.");
- }
-
- my $transcript_id = $transcript->dbID();
-
my $sth = $self->prepare( "INSERT into transcript_attrib ".
"SET transcript_id = ?, attrib_type_id = ?, ".
"value = ? " );
- for my $attrib ( @$attributes ) {
- if(!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
+ for my $attrib (@$attributes) {
+ if (!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
"argument expected.");
}
- my $atid = $self->_store_type( $attrib );
- $sth->bind_param(1,$transcript_id,SQL_INTEGER);
- $sth->bind_param(2,$atid,SQL_INTEGER);
- $sth->bind_param(3,$attrib->value,SQL_VARCHAR);
+ my $atid = $self->_store_type($attrib);
+ $sth->bind_param(1,$trans_dbID, SQL_INTEGER);
+ $sth->bind_param(2,$atid, SQL_INTEGER);
+ $sth->bind_param(3,$attrib->value, SQL_VARCHAR);
$sth->execute();
}
@@ -525,54 +505,44 @@ sub store_on_Transcript {
=head2 store_on_Translation
- Arg [1] : Bio::EnsEMBL::Translation $translation
+ Arg [1] : Int $transl_id
+ The dbID of the translation to store the attributes for
Arg [2] : listref Bio::EnsEMBL::Attribute $attribs
- Example : $attribute_adaptor->store_on_Translation($my_translation,
- $attributes)
+ Example : $attribute_adaptor->store_on_Translation($transl_id, $attributes)
Description: Stores all the attributes on the Translation.
Will duplicate things if called twice.
Returntype : none
Exceptions : throw on incorrect arguments
- throw if provided Translation is not stored in this database
Caller : general, TranslationAdaptor
Status : Stable
=cut
sub store_on_Translation {
- my $self = shift;
- my $translation = shift;
- my $attributes = shift;
-
- if(!ref($translation) || !$translation->isa('Bio::EnsEMBL::Translation')) {
- throw("Translation argument expected");
- }
+ my $self = shift;
+ my $transl_id = shift;
+ my $attributes = shift;
- if(ref($attributes) ne 'ARRAY') {
+ my $transl_dbID = $self->_id_check($transl_id);
+
+ if (ref($attributes) ne 'ARRAY') {
throw("Reference to list of Bio::EnsEMBL::Attribute objects argument " .
"expected");
}
- my $db = $self->db();
- if(!$translation->is_stored($db)) {
- throw("Translation is not stored in this DB - cannot store attributes.");
- }
-
- my $translation_id = $translation->dbID();
-
my $sth = $self->prepare( "INSERT into translation_attrib ".
"SET translation_id = ?, attrib_type_id = ?, ".
"value = ? " );
- for my $attrib ( @$attributes ) {
- if(!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
+ for my $attrib (@$attributes) {
+ if (!ref($attrib) && $attrib->isa('Bio::EnsEMBL::Attribute')) {
throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
"argument expected.");
}
- my $atid = $self->_store_type( $attrib );
- $sth->bind_param(1,$translation_id,SQL_INTEGER);
- $sth->bind_param(2,$atid,SQL_INTEGER);
- $sth->bind_param(3,$attrib->value,SQL_VARCHAR);
+ my $atid = $self->_store_type($attrib);
+ $sth->bind_param(1,$transl_dbID, SQL_INTEGER);
+ $sth->bind_param(2,$atid, SQL_INTEGER);
+ $sth->bind_param(3,$attrib->value, SQL_VARCHAR);
$sth->execute();
}
@@ -823,8 +793,37 @@ sub remove_from_Translation {
}
+#
+# _id_check
+#
+# backwards compatibility check:
+# check if $ensID is an object; if so, return $obj->dbID
+#
+
+sub _id_check {
+ 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') {
+ 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");
+ }
+
+ } else {
+ throw("Invalid dbID");
+ }
+
+}
# _store_type
@@ -865,13 +864,10 @@ sub _store_type {
$sth1->finish();
-
return $atid;
}
-
-
sub _obj_from_sth {
my $self = shift;
my $sth = shift;
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 7ce2013edc14debe89a4cd0684381cd8129eca27..401b346e13d4464aba9194a73b5094603251ebc3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -203,33 +203,56 @@ sub fetch_by_db_accession {
}
-
=head2 store
Arg [1] : Bio::EnsEMBL::DBEntry $exObj
The DBEntry (xref) to be stored
- Arg [2] : Bio::EnsEMBL::Transcript, Bio::EnsEMBL::Gene or
- Bio::EnsEMBL::Translation $ensObject
- An EnsEMBL object to associate with this external database entry
- Arg [3] : string $ensType ('Transcript', 'Translation', 'Gene');
+ Arg [2] : Int $ensID
+ The dbID of an EnsEMBL object to associate with this external
+ database entry
+ Arg [3] : string $ensType ('Transcript', 'Translation', 'Gene')
The type of EnsEMBL object that this external database entry is
being associated with.
- Example : $dbea->store($db_entry, $transcript, 'Transcript');
+ Example : $dbea->store($db_entry, $transcript_id, 'Transcript');
Description: Stores a reference to an external database (if it is not stored
already) and associates an EnsEMBL object of a specified type
with the external identifier.
- Returntype : int - the identifier of the newly created external refernce
- Exceptions : none
- Caller : scripts which load Xrefs and ObjectXrefs, etc. into EnsEMBL.
+ Returntype : int - the dbID of the newly created external refernce
+ Exceptions : thrown when invalid dbID is passed to this method
+ Caller : scripts which load Xrefs and ObjectXrefs, etc. into Ensembl
Status : Stable
=cut
-
sub store {
- my ( $self, $exObj, $ensObject, $ensType ) = @_;
+ my ( $self, $exObj, $ensID, $ensType ) = @_;
my $dbJustInserted;
+ #
+ # backwards compatibility check:
+ # check if $ensID is an object; if so, use $obj->dbID
+ #
+ my $ensembl_id;
+
+ if ($ensID =~ /^\d+$/) {
+ $ensembl_id = $ensID;
+
+ } elsif ( ref($ensID) eq 'Bio::EnsEMBL::Gene' or
+ ref($ensID) eq 'Bio::EnsEMBL::Transcript' or
+ ref($ensID) eq 'Bio::EnsEMBL::Translation') {
+
+ warning("You should pass DBEntryAdaptor->store() a dbID rather than an ensembl object to store the xref on");
+
+ if ($ensID->dbID) {
+ $ensembl_id = $ensID->dbID;
+ } else {
+ throw("$ensType ".$ensID->display_id." doesn't have a dbID, can't store xref");
+ }
+
+ } else {
+ throw("Invalid dbID passed to DBEntryAdaptor->store()");
+ }
+
#
# Check for the existance of the external_db, throw if it does not exist
#
@@ -328,7 +351,7 @@ sub store {
AND ensembl_id = ?");
$sth->bind_param(1,$dbX,SQL_INTEGER);
$sth->bind_param(2,$ensType,SQL_VARCHAR);
- $sth->bind_param(3,$ensObject->dbID,SQL_INTEGER);
+ $sth->bind_param(3,$ensembl_id,SQL_INTEGER);
$sth->execute();
my ($tst) = $sth->fetchrow_array;
$sth->finish();
@@ -342,7 +365,7 @@ sub store {
$sth->bind_param(1,$dbX,SQL_INTEGER);
$sth->bind_param(2,$ensType,SQL_VARCHAR);
- $sth->bind_param(3,$ensObject->dbID,SQL_INTEGER);
+ $sth->bind_param(3,$ensembl_id,SQL_INTEGER);
$sth->execute();
$exObj->dbID( $dbX );
@@ -630,7 +653,7 @@ sub remove_from_object {
=head2 _fetch_by_object_type
- Arg [1] : string $ensObj
+ Arg [1] : string $ensID
Arg [2] : string $ensType
(object type to be returned)
Example : $self->_fetch_by_object_type( $translation_id, 'Translation' )
@@ -646,10 +669,10 @@ sub remove_from_object {
=cut
sub _fetch_by_object_type {
- my ( $self, $ensObj, $ensType ) = @_;
+ my ( $self, $ensID, $ensType ) = @_;
my @out;
- if (!defined($ensObj)) {
+ if (!defined($ensID)) {
throw("Can't fetch_by_EnsObject_type without an object");
}
if (!defined($ensType)) {
@@ -677,7 +700,7 @@ sub _fetch_by_object_type {
AND oxr.ensembl_object_type = ?
");
- $sth->bind_param(1,$ensObj,SQL_INTEGER);
+ $sth->bind_param(1,$ensID,SQL_INTEGER);
$sth->bind_param(2,$ensType,SQL_VARCHAR);
$sth->execute();
my (%seen, %linkage_types, %synonyms);
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index db17e8dbd03f9adc7fe92ae0c22fa4b56e0ba8de..a428da13b630988dbec06f692d972f114799cfc1 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -823,10 +823,6 @@ sub store {
my $gene_dbID = $sth->{'mysql_insertid'};
- # set dbID and adaptor of gene here - you'll need this when storing xrefs
- $gene->dbID($gene_dbID);
- $gene->adaptor($self);
-
# store stable ids if they are available
if (defined($gene->stable_id)) {
@@ -834,18 +830,10 @@ sub store {
SET gene_id = ?,
stable_id = ?,
version = ?, ";
- $statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($gene->created_date()) . ",";
-# if( $gene->created_date() ) {
-# $statement .= "created_date = from_unixtime( ".$gene->created_date()."),";
-# } else {
-# $statement .= "created_date = \"0000-00-00 00:00:00\",";
-# }
- $statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($gene->modified_date());
-# if( $gene->modified_date() ) {
-# $statement .= "modified_date = from_unixtime( ".$gene->modified_date().")";
-# } else {
-# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
-# }
+ $statement .= "created_date = " .
+ $self->db->dbc->from_seconds_to_date($gene->created_date()) . ",";
+ $statement .= "modified_date = " .
+ $self->db->dbc->from_seconds_to_date($gene->modified_date());
$sth = $self->prepare($statement);
$sth->bind_param(1,$gene_dbID,SQL_INTEGER);
@@ -859,7 +847,7 @@ sub store {
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$gene->get_all_DBEntries} ) {
- $dbEntryAdaptor->store( $dbe, $gene, "Gene" );
+ $dbEntryAdaptor->store($dbe, $gene_dbID, "Gene");
}
# we allow transcripts not to share equal exons and instead have copies
@@ -928,15 +916,14 @@ sub store {
}
}
- # set the adaptor and dbID on the original passed in gene not the
- # transfered copy
- $original->adaptor( $self );
- $original->dbID( $gene_dbID );
-
# store gene attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
- $attr_adaptor->store_on_Gene($gene,
- $gene->get_all_Attributes);
+ $attr_adaptor->store_on_Gene($gene_dbID, $gene->get_all_Attributes);
+
+ # set the adaptor and dbID on the original passed in gene not the
+ # transfered copy
+ $original->adaptor($self);
+ $original->dbID($gene_dbID);
return $gene_dbID;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 485acb06b3a34364eaf6dda560490d3f8d0b9886..307074c427decaecb2d4a5aeef88d75fa9c90b48 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -604,11 +604,6 @@ sub store {
my $transc_dbID = $tst->{'mysql_insertid'};
- # set dbID and adaptor of transcript here - you'll need this when storing
- # xrefs
- $transcript->dbID($transc_dbID);
- $transcript->adaptor($self);
-
#
# store translation
#
@@ -666,7 +661,7 @@ sub store {
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
- $dbEntryAdaptor->store( $dbe, $transcript, "Transcript" );
+ $dbEntryAdaptor->store($dbe, $transc_dbID, "Transcript");
}
#
@@ -791,18 +786,16 @@ sub store {
$sf_sth->execute();
}
-
-
- #update the original transcript object - not the transfered copy that
- #we might have created
- $original->dbID( $transc_dbID );
- $original->adaptor( $self );
-
# store transcript attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
- $attr_adaptor->store_on_Transcript($transcript,
+ $attr_adaptor->store_on_Transcript($transc_dbID,
$transcript->get_all_Attributes);
+ #update the original transcript object - not the transfered copy that
+ #we might have created
+ $original->dbID($transc_dbID);
+ $original->adaptor($self);
+
return $transc_dbID;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index be72c5f7ee5e5d56f32a9e5ffdeb5d15016ae204..14c4fc7356e8ed3b9bbf7b835c4b814c67727a32 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -237,15 +237,13 @@ sub store {
my $transl_dbID = $sth->{'mysql_insertid'};
- $translation->dbID($transl_dbID);
- $translation->adaptor($self);
-
- #store object xref mappings to translations
-
+ #
+ # store object xref mappings to translations
+ #
my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();
- #store each of the xrefs for this translation
+ # store each of the xrefs for this translation
foreach my $dbl ( @{$translation->get_all_DBEntries} ) {
- $dbEntryAdaptor->store( $dbl, $translation, "Translation" );
+ $dbEntryAdaptor->store( $dbl, $transl_dbID, "Translation" );
}
@@ -259,19 +257,10 @@ sub store {
"SET translation_id = ?, ".
" stable_id = ?, ".
"version = ?, ";
- $statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($translation->created_date()) . ",";
-
-# if( $translation->created_date() ) {
-# $statement .= "created_date = from_unixtime( ".$translation->created_date()."),";
-# } else {
-# $statement .= "created_date = \"0000-00-00 00:00:00\",";
-# }
- $statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($translation->modified_date()) ;
-# if( $translation->modified_date() ) {
-# $statement .= "modified_date = from_unixtime( ".$translation->modified_date().")";
-# } else {
-# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
-# }
+ $statement .= "created_date = " .
+ $self->db->dbc->from_seconds_to_date($translation->created_date()) . ",";
+ $statement .= "modified_date = " .
+ $self->db->dbc->from_seconds_to_date($translation->modified_date()) ;
my $sth = $self->prepare($statement);
@@ -287,9 +276,11 @@ sub store {
# store any translation attributes that are defined
my $attr_adaptor = $self->db->get_AttributeAdaptor();
- $attr_adaptor->store_on_Translation($translation,
+ $attr_adaptor->store_on_Translation($transl_dbID,
$translation->get_all_Attributes());
+ $translation->dbID($transl_dbID);
+ $translation->adaptor($self);
return $transl_dbID;
}
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index 8152408221c4bd623e6f9edcecb02acf02ebf226..7e939f56be849d387563f6ba7d9c6dd8c6b7d444 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -73,7 +73,7 @@ ok( $db_entry_count == $xref_count );
#
# 4,5 correct number of GoXrefs and IdentityXrefs
#
-print $goxref_count . " " . $ident_count . "\n";
+debug( "GoXrefs and IdentityXrefs: ".$goxref_count . " " . $ident_count);
ok( $goxref_count == 48 );
ok( $ident_count == 32 );
@@ -126,11 +126,11 @@ my $gene = $ga->fetch_by_dbID( $all_gene_ids->[0] );
my $tr = $gene->get_all_Transcripts()->[0];
my $tl = $tr->translation();
-$dbEntryAdaptor->store( $xref, $gene, "Gene" );
-$dbEntryAdaptor->store( $xref, $tr, "Transcript" );
-$dbEntryAdaptor->store( $goref, $tl, "Translation" );
-$dbEntryAdaptor->store( $ident_xref, $tl, "Translation" );
-$dbEntryAdaptor->store( $ident_xref, $tr, "Transcript" );
+$dbEntryAdaptor->store( $xref, $gene->dbID, "Gene" );
+$dbEntryAdaptor->store( $xref, $tr->dbID, "Transcript" );
+$dbEntryAdaptor->store( $goref, $tl->dbID, "Translation" );
+$dbEntryAdaptor->store( $ident_xref, $tl->dbID, "Translation" );
+$dbEntryAdaptor->store( $ident_xref, $tr->dbID, "Transcript" );
my ( $oxr_count, $go_count );
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 7d5d6177d4984908abe8b38534ad71f36d7010c6..87ee6388d44031b7efeb5ed4a148b7b170980026 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -110,7 +110,9 @@ ok($analysis);
$gene = Bio::EnsEMBL::Gene->new();
my $transcript1 = Bio::EnsEMBL::Transcript->new();
+$transcript1->analysis($analysis);
my $transcript2 = Bio::EnsEMBL::Transcript->new();
+$transcript2->analysis($analysis);
my $ex1 = Bio::EnsEMBL::Exon->new();
my $ex2 = Bio::EnsEMBL::Exon->new();
@@ -563,10 +565,11 @@ my $second_ex = Bio::EnsEMBL::Exon->new
$transcript1 = Bio::EnsEMBL::Transcript->new
(-EXONS => [$first_ex, $second_ex]);
+$transcript1->analysis($analysis);
$transcript2 = Bio::EnsEMBL::Transcript->new
(-EXONS => [$first_ex]);
-
+$transcript2->analysis($analysis);
$gene->add_Transcript($transcript1);
$gene->add_Transcript($transcript2);
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index 167edabfbedb5b9caaab0888b73bca90e1701e54..7c35b3acdf014fcd8512b7f5da308f85da5417a5 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -410,7 +410,7 @@ ok($tr->translateable_seq() eq $tlseq1);
$multi->hide( "core", "transcript_attrib" );
my $attribAdaptor = $db->get_AttributeAdaptor();
-$attribAdaptor->store_on_Transcript( $tr, $tr->get_all_Attributes() );
+$attribAdaptor->store_on_Transcript($tr->dbID, $tr->get_all_Attributes);
$tr = $ta->fetch_by_stable_id( "ENST00000217347" );
$tr->edits_enabled(1);
diff --git a/modules/t/translation.t b/modules/t/translation.t
index 326256c2ee844e8131f46f39db44c8a255e00998..13ba721b62d9d11f7b36b3a2342aa28c4f126ec6 100644
--- a/modules/t/translation.t
+++ b/modules/t/translation.t
@@ -200,7 +200,7 @@ $multi->hide( "core", "translation_attrib" );
my $tl = $tr->translation();
my $attrAdaptor = $db->get_AttributeAdaptor();
-$attrAdaptor->store_on_Translation( $tl, $tl->get_all_Attributes() );
+$attrAdaptor->store_on_Translation($tl->dbID, $tl->get_all_Attributes);
$tr = $tra->fetch_by_stable_id( "ENST00000217347" );