From 465d3bc04ae1932618c6f8e190496c7ca3725a8d Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 22 May 2013 16:09:26 +0000
Subject: [PATCH] [ENSCORESW-476]. Fixed backwards compatibility for anything
which is older than release 72
---
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm | 17 +++++++++
.../Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm | 2 +-
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 37 +++++++++++++++----
3 files changed, 48 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index 84ac9a1e4f..d2f514093b 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -845,6 +845,23 @@ sub ignore_cache_override {
return $self->{'_override'};
}
+=head2 schema_version
+
+ Description : Returns the schema version of the currently connected
+ DBAdaptor. The subroutine also caches this value so
+ repeated calls continue to be speedy.
+ Example : $adaptor->schema_version();
+ Returntype : Integer
+
+=cut
+
+sub schema_version {
+ my ($self) = @_;
+ return $self->{_schema_version} if exists $self->{_schema_version};
+ my $mc = $self->db()->get_MetaContainer();
+ return $self->{_schema_version} = $mc->get_schema_version();
+}
+
#_tables
#
# Args : none
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
index 533e89db1b..2141128a72 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
@@ -72,7 +72,7 @@ sub get_schema_version {
if ( !defined($ver) ) { # old style format
return 0;
}
- return $ver;
+ return $ver * 1; #multiply by 1 to get this into a number
} else {
warning(
sprintf(
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index da3a037d56..7534338c72 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -1282,8 +1282,11 @@ sub _fetch_by_object_type {
throw("Can't fetch_by_EnsObject_type without a type");
}
+ ### TODO - SCHEMA VERSION HACK. Please remove sometime in the future once we do not want backwards compatibility
+ my $schema_version = $self->schema_version();
+
# my $sth = $self->prepare("
- my $sql = (<<SSQL);
+ my $columns_sql = (<<COLUMNS_SQL);
SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
exDB.priority,
exDB.db_name, exDB.db_release, exDB.status, exDB.db_display_name,
@@ -1295,20 +1298,40 @@ sub _fetch_by_object_type {
idt.cigar_line, idt.score, idt.evalue, oxr.analysis_id,
gx.linkage_type,
xref.info_type, xref.info_text, exDB.type, gx.source_xref_id,
- oxr.linkage_annotation, xref.description,
- ax.xref_id, ax.source_xref_id, ax.condition_type,
- ax.associated_group_id, ax.rank
+ oxr.linkage_annotation, xref.description
+COLUMNS_SQL
+
+ my $tables_sql = <<'TABLES_SQL';
FROM (xref xref, external_db exDB, object_xref oxr)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
LEFT JOIN ontology_xref gx on gx.object_xref_id = oxr.object_xref_id
- LEFT JOIN associated_xref ax ON ax.object_xref_id = oxr.object_xref_id
- LEFT JOIN associated_group ag ON ax.associated_group_id = ag.associated_group_id
+TABLES_SQL
+
+ my $where_sql = <<'WHERE_SQL';
WHERE xref.xref_id = oxr.xref_id
AND xref.external_db_id = exDB.external_db_id
AND oxr.ensembl_id = ?
AND oxr.ensembl_object_type = ?
-SSQL
+WHERE_SQL
+
+ if($schema_version >= 72) {
+ $columns_sql .= ','; #need the extra comma
+ $columns_sql .= <<'EXTRA';
+ ax.xref_id, ax.source_xref_id, ax.condition_type, ax.associated_group_id, ax.rank
+EXTRA
+ $tables_sql .= <<'EXTRA';
+ LEFT JOIN associated_xref ax ON ax.object_xref_id = oxr.object_xref_id
+ LEFT JOIN associated_group ag ON ax.associated_group_id = ag.associated_group_id
+EXTRA
+
+ }
+
+ #Join the above together into one statement
+ my $sql = "$columns_sql
+$tables_sql
+$where_sql";
+ # warn $sql; # uncomment me to see the full SQL generated
if ( defined($exdbname) ) {
if ( index( $exdbname, '%' ) != -1 ) {
--
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