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Commit e992cd08 authored by Monika Komorowska's avatar Monika Komorowska
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Field dbprimary_acc_linkable removed from external_db.

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modules/Bio/EnsEMBL/DBEntry.pm
+ 3
− 26
View file @ e992cd08
......@@ -83,7 +83,6 @@ sub new_fast {
-release => $release,
-display_id => $did,
-description => $description,
-primary_id_linkable =>$primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......@@ -97,7 +96,7 @@ sub new_fast {
Exceptions : none
Caller : Bio::EnsEMBL::DBEntryAdaptor
Status : At Risk
Due to 'PRIMARY_ID_LINKABLE','PRIORITY',
Due to 'PRIORITY',
'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'TYPE',
'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE'
being under development - if you don't use any of these the
......@@ -112,12 +111,12 @@ sub new {
my ( $adaptor, $dbID, $primary_id, $version,
$dbname, $release, $display_id, $description,
$primary_id_linkable, $priority,
$priority,
$db_display_name, $info_type, $info_text, $type,
$secondary_db_name, $secondary_db_table, $link_annotation, $analysis) =
rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
'PRIMARY_ID_LINKABLE', 'PRIORITY',
'PRIORITY',
'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT', 'TYPE',
'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE', 'LINKAGE_ANNOTATION', 'ANALYSIS'], @args );
......@@ -131,7 +130,6 @@ sub new {
if( defined $release) { $self->release( $release ) }
if( defined $display_id) { $self->display_id( $display_id ) }
if( defined $description) { $self->description($description) }
if( defined $primary_id_linkable) { $self->primary_id_linkable($primary_id_linkable) }
if( defined $priority) { $self->priority($priority) }
if( defined $db_display_name) { $self->db_display_name($db_display_name) }
if( defined $info_type) { $self->info_type($info_type) }
......@@ -361,27 +359,6 @@ sub comment {
}
=head2 primary_id_linkable
Arg [1] : (optional) Boolean $arg - value to set
Example : none
Description: Getter/setter for attribute 'primary_id_linkable'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
: due to it being under development
=cut
sub primary_id_linkable {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{primary_id_linkable} = $arg;
}
return $self->{primary_id_linkable};
}
=head2 priority
Arg [1] : int $priority
......
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+ 2
− 19
View file @ e992cd08
......@@ -78,7 +78,6 @@ sub fetch_by_dbID {
xref.dbprimary_acc,
xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable,
exDB.priority,
exDB.db_name,
exDB.db_display_name,
......@@ -108,7 +107,6 @@ sub fetch_by_dbID {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $refID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$dbname, $db_display_name,
$release, $synonym,
......@@ -127,7 +125,6 @@ sub fetch_by_dbID {
-version => $version,
-release => $release,
-dbname => $dbname,
-primary_id_linkable => $primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......@@ -172,7 +169,6 @@ sub _get_all_dm_loc_sth {
xref.dbprimary_acc,
xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable,
exDB.priority,
exDB.db_name,
exDB.db_display_name,
......@@ -211,7 +207,6 @@ sub _get_all_dm_sth {
xref.dbprimary_acc,
xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable,
exDB.priority,
exDB.db_name,
exDB.db_display_name,
......@@ -258,7 +253,6 @@ sub _get_all_dm{
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$dbname, $db_display_name,
$release, $synonym,
......@@ -277,7 +271,6 @@ sub _get_all_dm{
-version => $version,
-release => $release,
-dbname => $dbname,
-primary_id_linkable => $primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......@@ -401,7 +394,6 @@ sub fetch_by_db_accession {
xref.dbprimary_acc,
xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable,
exDB.priority,
exDB.db_name,
exDB.db_display_name,
......@@ -455,7 +447,6 @@ sub fetch_by_db_accession {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$dbname, $db_display_name,
$release, $synonym,
......@@ -474,7 +465,6 @@ sub fetch_by_db_accession {
-version => $version,
-release => $release,
-dbname => $dbname,
-primary_id_linkable => $primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......@@ -1102,7 +1092,6 @@ sub _fetch_by_object_type {
# my $sth = $self->prepare("
my $sql = (<<SSQL);
SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
exDB.dbprimary_acc_linkable,
exDB.priority,
exDB.db_name, exDB.db_release, exDB.status, exDB.db_display_name,
exDB.secondary_db_name, exDB.secondary_db_table,
......@@ -1158,7 +1147,6 @@ SSQL
while ( my $arrRef = shift( @{$rowcache} ) ) {
my ( $refID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$dbname, $release,
$exDB_status, $exDB_db_display_name,
......@@ -1238,7 +1226,6 @@ SSQL
if ( defined($exDB_status) ) { $exDB->status($exDB_status) }
$exDB->primary_id_linkable($primary_id_linkable);
$exDB->priority($priority);
$exDB->db_display_name($exDB_db_display_name);
......@@ -1671,7 +1658,7 @@ sub fetch_all_by_description {
my $sql =
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable, exDB.priority,
exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
xref.info_type, xref.info_text, exDB.type, exDB.secondary_db_name,
exDB.secondary_db_table, xref.description
......@@ -1698,7 +1685,6 @@ sub fetch_all_by_description {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$ex_dbname, $db_display_name,
$release, $synonym,
......@@ -1716,7 +1702,6 @@ sub fetch_all_by_description {
-version => $version,
-release => $release,
-dbname => $ex_dbname,
-primary_id_linkable => $primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......@@ -1762,7 +1747,7 @@ sub fetch_all_by_source {
my $sql =
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version,
exDB.dbprimary_acc_linkable, exDB.priority,
exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
xref.info_type, xref.info_text, exDB.type, exDB.secondary_db_name,
exDB.secondary_db_table, xref.description
......@@ -1784,7 +1769,6 @@ sub fetch_all_by_source {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$primary_id_linkable,
$priority,
$dbname, $db_display_name,
$release, $synonym,
......@@ -1802,7 +1786,6 @@ sub fetch_all_by_source {
-version => $version,
-release => $release,
-dbname => $dbname,
-primary_id_linkable => $primary_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
......
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